Genome Detective

NGS Details (SRR3458562_Metagenome_example): Koala retrovirus

Assembly

Coverage Length

2112 (2 contig(s))

Depth Of Coverage

16.0

Number Of Reads

313

Reads Per Million

20.20 rpm (after QC)

Ambiguities

Assembly Method

de novo + reference guided assembly

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants

Download consensus variants (vcf)

Minority Variants

Download minority variants (vcf)

SNP Variants Table

Download SNP mutations table (csv)

Annotated Variants Table

Download annotated variants table (csv)

Assignment

Type

Koala retrovirus (Taxonomy ID: 394239)

Reference Genome

NC_039228.1

NT Identity (%)

66.9484

AA Identity (%)

71.4076

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

1417.0 (NT) + 3557.0 (AA) = 4974.0

Concordance (%)

55.8751

Alignment Method

Global, seeded, nucleotide + amino acids (AGA)

NT Alignment

Download alignment (FASTA)

Region Bam File

Download BAM zip file

CDS Alignment

Download CDS alignment (FASTA)

Consensus Sequence

Download consensus sequence (FASTA) (Including IUPAC ambiguity codes)

Consensus Contigs

Download consensus contigs (FASTA)

Genome Region

Sequence starts at position 1597 and ends at position 3737 relative to NC_039228.1 reference sequence.

NC_039228.1

SRR3458562_Metagenome_example-NC_039228.1-112-0

NC_039228.1

SRR3458562_Metagenome_example-NC_039228.1-112-0

NC_039228.1

SRR3458562_Metagenome_example-NC_039228.1-112-0

AATGAAGGAGGCAGAAATCATGAGGCAGAAATCATTCCGTGGAGTATGGAAACTACCCGGAGGGCCCAAGGTTTAGGGACAGGTGCAGCCAGGCACAGTAAAAGGTCAGAGCAAGAAAAACAAGGAAGATTTGGAGTGCCAAACGGGATATCTGTGGTCATGCACCTGAGTCCCCACCCCGGACTTATGCAAACAATTCCCAGAAATAGCTGAGCTCATAACAGTTTCTAGGGTGCCCCTCAGCAGTTTCTAGAACCCTCTCGTGACCGGAGTTTTTATTCAAACTAACCAATGATCTTGCTCCTCGCTTCCGTACCCGCGCTTTTTTGCTATAAAATGAGACCAAAGAATCCACCTGGCGCGCCAGTCCCTCTAGGTGACTGAGTCGCCCGAGTACTCGTAAGTTCAATAAACCTCTTGCTATTTGCATCCGGAGTTGTGTTCGCGTTGATCCTGGGAGGGTTTCTCAAGGTCGGAGGACTACCCGAACATTGGGGTCTTTCATTTGGGGGCTCGTCCGGGATCTGAGATTCCCACCCAAGGACCGCCGAACCACCGACGGGAGGTAAGCTGGCCAGCGATCGCTCTATGTTCTCTCTGTGTCTGACTCCGAAAACTCTGACTGTCTATTCGGTGTGCGCGCATTTTTGGTTTATTCCGGGTTAATCGATCTAAGATCGAGGCGTGAGTAGCGGACAGACGTGTTCGGGGGCTCACCGCCCGGCAATCCTGGGAGACGTCCCAGGATCAGGGGAGGACCAGGGACGCCTGGTGGATCCCACGGCAAGGGATAATTCTCCTCTGATCTCACAGTTGCACTGTCTTGAGAGACATACCCTACCTTCTGACTCTTTTTCCTGTCTTTTTAATATACGTCTACGCCGCCATATAATTTTTTTCCTTTTTATTTCAATAATAATCATTATCTGGGTCGTAATTCCACTCTTCGGGACCCCCAGAATGGGACAGGGTGAGTCGACCCCTCTCTCTCTTACACTAG

ATCACTGGAAAGACGTGAAGACAAGGGCTCACAATCTTTCCGTGGAGATAAGAAAGGGAAAGTGGCAAACCTTCTGTTCCTCCGAGTGGCCCACGTTCGAAGTGGGATGGCCACCGGAGGGGACTTTTAATCCTTCTATTATTTCTGCAGTCAAAAGGATTGTCTTCCAGGAGACTGGAGGACACCCGGACCAGGTTCCCTACATCATAGTTTGGCAGGACCTCTCCAACAGCCCCCCCCCATGGGTGCCACCCTTAGCCAAGATCGCCGTTGCCTCTGGTCAAGATAACGGGCGAAAGTCGGCGGGGGGGAGGCCGTCCGCTCCTTCCCGGCTCCCCATCTACCCGGAGACGGACAGCCTGTTCCTCCTCTCAGAACCCCCGCCCTATCCAACGTCCCCTCCACCTCCCCCAGCCCCTCACGCGGCCAGACCAGCGCCAGGCCTAATGGCTGAGGGACTCGGCTCTGAGGGACCGGCCGCTGGAACTAGGAGTCGCCGTCCCCGCAGTCCTACGGGTGACACTGGTCCTGACTCCACTGTGGCCCTGCCCCTCCGGGCCGTGGGACCCCCGGCCGAACCAAACGGCTTAGTCCCCTTGCAATATTGGCCTTTCTCCTCAGCAGATCTCTATAATTGGAAATCTAATCATCCTTCTTTTTCCGAGAATCCTACAGGACTTACGGGACTCCTTGAGTCCCTCATGTTTTCCCACCAGCCTACTTGGGACGATTGCCAGCAGCTCCTGCAAGTCCTCTTTACCACCGAGGAAAGAGAAAGGATTCTTTTGGAGGCTCGCAAAAACGTCCTTGGAGTTAACGGGGCCCCTACACAACTCGAGAACCTCATTAATGAGGCCTTCCCCCTTAATCGACCTCAGTGGGATCACAACACGGCTGAAGGTAGGGAGCGTCTCCTGGTCTACCGCCGGACTCTAGTGGCGGGTCTCAAAGGGGCAGCAAGGCGCCCCACCAATTTGGCCAAGGTAAGAGAAGTCTTGCA

GGGACCAACAGAACCCCCGTCCGTTTTTCTAGAACGTCTAATGGAGGCTTATAGGAGATATACCCCATTTGATCCCTCTTCTGAGGGACAAAAGGCGGCGGTGGCCATGTCCTTTATCGGGCAGTCTGCCCCGGATATTAAAAAGAAATTACAAAGGCTGGAAGGACTCCAGGACCATTCCTTGCAGGATCTCATAAAGGAGGCAGAGAAGGTATATCATAAGAGAGAGACAGAGGAAGAAAAGCAAGAAAGAGAGAAAAAGGAGACAGAGGAAAGAGAGAGACGGCGTGACAGGCGCCAGGAGAAAAACTTGACCAAAATCTTGGCCGCGGTAGTAAGTGAGAAAGGGTTCAGAGGGAGACAGGCAGGGAATCTGAGCAACAGGGCAATGAGGGCACCTAGGGAAGGA---------------AGACCGCCTCTGGACAAAGATCAGTGCGCATACTGTAAAGAAAGGGGCCATTGGGCAAGGGAGTGCCCCCGGAAGAAGAACGCCAGGGAAACCAATGTCCTGACCCTGGGT---------GACTAGGGGAGTCGGGGTTCGGACCCCCTCCCCGAGCCCAGGGTAACGTTAACTGTGGAGGGGATCCCCACTGAGTTTTTGGTTGATACCGGGGCCGAACATTCAGTATTGACCAAGCCTATGGGAAAGATGGGATCCAAACGGACAGTCGTGGCTGGGGCGACGGGCAGCAAAGTTTACCCTTGGACCACCAAGAGACTTTTGAAAATTGGACAAAAGCAAGTGACCCACTCATTCTTGGTCATACCCGAATGCCCTGCTCCCCTGTTAGGCAGGGACCTCCTCACCAAGCTAAAAGCTCAAATCCAGTTTTCCACAGAGGGCCCACAGGTAACATGGGAAGACCGCCCCGCCATGTGTTTAGTCCTGAACTTGGAGGAGGAATACCGATTACACGAAAAGCCGGTCCCTCCTTCTATCGAC---CCGTCATGGCTCCAACTCTTTCCCATGGTT

TGGGCCGAGAAGGCAGGTATGGGACTGGCCAATCAAGTCCCACCAGTGGTAGTGGAACTGAAGTCAGATGCCTCACCAGTGGCTGTTCGACAGTACCCAATGAGCAAGGAAGCCCGGGAGGGTATCAGGCCCCACATCCAAAGATTCTTGGATTTGGGGATTCTGGTACCTTGCCAGTCGCCCTGGAACACCCCTTTGTTACCTGTAAAAAAACCTGGAACCAATGACTATCGGCCAGTCCAAGATTTGAGGGAGGTCAACAAAAGAGTACAGGACATTCATCCCACAGTCCCGAACCCCTATAACCTACTCAGTTCCCTCCCGCCCAGCCACACCTGGTATTCAGTTTTAGACCTCAAAGATGCTTTCTTTTGCCTCAAGCTACACCCCAACAGCCAGCCATTGTTCGCGTTTGAATGGAGAGATCCAGAAAAAGGCAATACTGGCCAGCTAACCTGGACTCGGCTACCGCAAGGATTCAAGAACTCTCCCACCCTCTTCGATGAGGCCCTCCACCGGGATCTGGCATCCTTCAGGGCTCTCAACCCCCAGGTAGTGATGCTCCAATATGTTGATGACCTCCTGGTAGCGGCCCCAACGTACCGAGACTGCAAAGAAGGGACACGAAGGCTCTTACAGGAACTAAGTAAGTTGGGATACCGAGTGTCGGCCAAAAAGGCCCAGCTTTGCCGGGAGGAAGTTACGTATCTCGGGTATTTGCTAAAAGGGGGGAAGAGATGGCTGACCCCAGCCCGAAAGGCCACTGTAATGAAGATCCCCACCCCTACAACCCCCAGACAAGTCCGTGAGTTTTTGGGCACTGCTGGATTCTGTAGGCTCTGGATCCCTGGTTTCGCTTCCCTGGCTGCACCCCTGTACCCCCTGACGAGAGAAAAGGTTCCCTTTACCTGGACTGAGGCCCACCAGGAAGCCTTTGGCCGTATAAAAGAGGCCCTGCTATCGGCCCCCGCCCTGGCCCTTCCGGACCTCACCAAGCCAT

TTGCTCTGTACGTGGATGAAAAAGAGGGTGTTGCCCGGGGGGTGCTTACTCAAACCCTAGGACCATGGCGACGCCCGGTAGCTTACCTGTCAAAAAAATTAGATCCGGTGGCCAGTGGGTGGCCAACTTGCCTAAAAGCAATTGCGGCCGTAGCACTCCTTCTCAAGGACGCTGATAAGTTAACCCTAGGACAGAACGTGTTGGTGATTGCACCTCACAACCTGGAAAGCATTGTGAGACAGCCCCCCGACCGATGGATGACAAATGCCAGGATGACCCATTACCAAAGTCTGCTGCTGAATGAGAGGGTGTCTTTTGCGCCCCCGGCCATTCTGAATCCTGCCACCCTGCTCCCCGTAGAGTCAGACGACACCCCAATACACATATGCTCAGAAATCCTTGCCGAGGAGACAGGAACCCGACCTGATCTGAGAGATCAGCCGTTGCCCGGGGTACCCGCTTGGTATACGGATGGCAGCAGTTTCATCATGGATGGCAGGCGACAAGCAGGTGCTGCCATTGTGGACAACAAGCGGACGGTGTGGGCGAGCAACCTGCCAGAGGGAACGTCAGCTCAGAAGGCCGAACTAATCGCCTTGACACAAGCATTACGCTTGGCCGAAGGAAAAAGCATCAACATCTACACGGACAGCAGGTACGCTTTTGCCACCGCTCATGTTCACGGGGCTATATACAAACAAAGAGGACTGCTCACTTCCGCTGGAAAAGACATCAAGAACAAAGAGGAGATTTTGGCCCTGCTAGAGGCCATCCATCTCCCTAAGCGAGTCGCTATCATCCATTGCCCCGGCCACCAAAGAGGGACTGACCCTGTGGCTACCGGAAACCGAAAGGCCGATGAGGCCGCGAAACAAGCTGCCCAGTCAACCAGAATACTGACGGAGACCACGAAAAATCAAGAACACTTCGAGCCTACACGGGGGAAGATCAAGCCGAGAGAGCTCACCCCTGACCAGGGAAGGGAATTCATTCAACGGCT

GCATCAGCTCACGCACTTAGGGCCAGACAAGCTTCTCCAGCTTGTAGGTCGCACCAGTTTTCACATCCCGAATCTCCAGTCTGTAGTGCGTGAAATCACCAGCAAGTGTCAGGTTTGTGCTGTAACTAACGCAGTCACCACCTACCGAGAGCCTGGAAGGAGGCAAAGGGGAGATCGACCCGGCGTGTATTGGGAAGTAGACTTCACAGAGGTTAAGCCTGGCCGGTATGGTAATAGATATTTGCTAGTGTTTATCGATACATTTTCTGGGTGGGTAGAAGCTTTCCCTACAAAAACAGAGACAGCCCTGACCGTCTGCAAGAAGATACTTGAGGAAATCCTACCTCGTTTCGGGATCCCTAAGGTACTCGGGTCCGACAATGGCCCTGCCTTCGTTGCTCAGGTAAGCCAGGGGTTGGCCACTCAACTGGGGATTGATTGGAAATTACATTGTGCATATAGACCCCAGAGCTCAGGTCAGGTAGAAAGGATGAATAGGACAATTAAAGAGACCTTGACAAAATTGGCCTTAGAGACCGGTGGAAAAGACTGGGTGACCCTCCTCCCTTTGGCGCTACTTAGGGCCCGGAATACCCCTGGCCAGTTTGGCCTGACTCCTTATGAGATTCTTCATGGGGGGCCGCCCCCTGTACTTGCGTCTGGGGAAGTCGTGGGTTCTAATGGTGATTTTTTTCCCGTTCTATTTACCCACTTGAAGGCTTTAGAGGTTGTGAGGACTCAGATCTGGGACCAGATAAAAGAAGCCTACAGGCCTGGTACTGTGGCCATTCCCCACCCGTTCCAGGTCGGTGACCGAGTGCTGGTTAGACGTCATCGGTCCGGCAGCCTTGAGCCTCGGTGGAAAGGCCCATACCTGGTGCTACTGACCACCCCGACCGCGGTGAAGGTTGACGGTATTGCTGCCTGGGTCCATGCTTCTCATCTCAAACCCGCGCCACCTGGGGCACCCGATGAGTCCTGGGAACTGGAAAAGACTGAT

CATCCTCTTAAGTTGCGTGTTCGGCGGCGCCGAAATGAATCAACAGCATAACAACCCTCACCAACCCATGACTCTCACCTGGCAGGTACTGTCCCAGACGGGAAGTGTCGTTTGGGAAAAGAAAGCAGTCGAGCCACCCTGGACGTGGTGGCCCTCTCTTGAGCCTGATGTGTGCGCGCTGGTAGCCGGTCTCGAGTCCTGGGACATCCCGGAACTCACTGCATCGGCCTCTCAACAGGCCAGGCCCCCTGATTCAAACTATGAACATGCTTATAATCAGATCACTTGGGGAACCCTGGGATGTAGCTATCCCCGGGCCAGAACAAGAATTGCTAGGTCCCAGTTCTACGTGTGCCCCCGGGATGGCCGTTCCCTGTCCGAGGCCCGGAGGTGCGGAGGACTTGAATCTTTGTACTGTAAAGAGTGGGGTTGTGAGACCGCGGGAACCGCCTACTGGCAACCCCGGTCCTCGTGGGACCTTATAACTGTAGGCCAGGGTCACCCTACAGGGACATGCGAGCGCACCGGTTGGTGCAACCCACTCAAGATAGAGTTCACCGAGCCTGGCAAACGGTTCCGAAACTGGCTACAGGGGCGAACCTGGGGTCTAAGGTTCTATGTGACTGGACACCCAGGCGTGCAGTTGACCATACGACTAGTGATCACAAGTCCCCCACCGGTAGTAGTGGGCCCCGATCCTGTCCTCGCAGAACAAGGACCTCCCAGAAAAATTCCCTTCCTCCCCAGAGTGCCGGTTCCTACCCTATCACCCCCAGCGTCCCCTATCCCCACGGTACAGGCTAGCCCCCCGGCCCCTAGTACTCCATCTCCCACCACGGGCGACCGGCTCTTTGGCCTCGTACAAGGGGCCTTTCTGGCCTTGAATGCCACCAACCCGGAGGCCACGGAGTCTTGCTGGCTCTGTCTAGCCCTCGGCCCTCCTTATTACGAAGGAATCGCAACTCCAGGGCAAGTCACTTATGCCTCCACAGATTCCCAA

TGTCGCTGGGGAGGAAAAGGGAAGCTCACCCTCACTGAAGTCTCTGGACTCGGGTTATGTATAGGGAAAGTACCTCCTACTCACCAACATCTCTGCAACCTGACTATACCCTTAAACGCCTCACATACTCACAAGTACCTCCTCCCCTCCAACCGCAGCTGGTGGGCTTGTAATTCTGGCCTCACCCCCTGCCTCTCTACATCAGTCTTCAACCAGTCTAACGATTTCTGTATCCAGATCCAGCTTGTCCCTCGCATCTACTATCACCCAGACGGTACCTTGCTACAGGCCTATGAGTCCCCCCACTCTAGAAACAAGAGAGAGCCTGTCTCACTCACCCTGGCTGTCCTTCTCGGATTAGGGGTCGCAGCAGGTATAGGTACCGGCTCGACCGCCCTAATAAAAGGGCCCATAGACCTCCAACAAGGTTTGACTAGCCTCCAGATTGCCATGGATACAGACCTTAGGGCCCTTCAAGACTCCATAAGTAAACTAGAGGATTCCTTAACCTCCCTGTCTGAAGTAGTGCTCCAGAATAGGAGAGGCCTTGATCTGCTATTTTTGAAGGAAGGGGGCCTTTGTGCAGCCCTAAAAGAGGAATGCTGTTTCTATGTTGACCACTCAGGCGCGGTGCGAGACTCCATGAGGAGACTCAAGGAAAGGTTAGATAAGAGGCAGTTAGAGCACCAAAAGAATTTAAGTTGGTACGAGGGATGGTTCAACCGTTCCCCCTGGCTTACTACTTTACTGTCTGCCCTTGCTGGTCCCCTGCTACTCCTCCTTCTGTTACTCACCCTCGGGCCTTGTGTCATCAATAAGTTAGTGCAATTCATCAATGATAGGGTTAGTGCAGTAAGGATTCTGGTTCTCAGGCACAAGTACCAGACCCTAGACAACGAGGATAACCTTTAATTCTGCTCTATGATTAGAGCTACCCTCAAAGAAAATGGGGGAATGAAGGAGGCAGAAATCATGAGGCAGAAATCATTCCGTGGAGTAT

GGAAACTACCCGGAGGGCCCAAGGTTTAGGGACAGGTGCAGCCAGGCACAGTAAAAGGTCAGAGCAAGAAAAACAAGGAAGATTTGGAGTGCCAAACGGGATATCTGTGGTCATGCACCTGAGTCCCCACCCCGGACTTATGCAAACAATTCCCAGAAATAGCTGAGCTCATAACAGTTTCTAGGGTGCCCCTCAGCAGTTTCTAGAACCCTCTCGTGACCGGAGTTTTTATTCAAACTAACCAATGATCTTGCTCCTCGCTTCTGTACCCGCGCTTTTTTGCTATAAAATGAGACCAAAGAATCCACCCGGCGCGCCAGTCCCTCTAGGTGACTGAGTCGCCCGAGTACTCGTAAGTTCAATAAACCTCTTGCTATTTGCATCCGGAGTTGTGTTCGCGTTGATCCTGGGAGGGTTTCTCAAGGTCAGAGGACTACCCGAACATTGGGGTCTTTCAT

........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGGCGGTATTGGCCCTTTTCTTCTGCAGATCTCTATAATTGGAAAACTAACCATCCCCCTTTCTCGGAGGATCCCCAACGCCTCACGGGGTTGGTGGAGTCCCTTATGTTCTCTCACCAGCCTACTTGGGATGATTGTCAACAGCTGCTGCAGACACTCTTCACAACCGAGGAGCGAGAGAGAATTCTGTTAGAGGCTAGAAAAAATGTTCCTGGGGCCGACGGGCGACCCACGCAGTTGCAAAATGAGATTGACATGGGATTTCCCTTGACTCGCCCCGGTTGGGACTACAACACGGCTGAAGGTAGGGAGAGCTTGAAAATCTATCGCCAGGCTCTGGTGGCGGGTCTCCGGGGCGCCTCAAGACGGCCCACTAATTTGGCTAAGGTAAGAGAGGTGATGCA

GGGACCGAACGAACCTCCCTCGGTATTTCTTGAGAGGCTCATGGAAGCCTTCAGGCGGTTCACCCCTTTTGATCCTACCTCAGAGGCCCAGAAAGCCTCAGTGGCCCTGGCCTTCATTGGGCAGTCGGCTCTGGATATCAGGAAGAAACTTCAGAGACTGGAAGGGTTACAGGAGGCTGAGTTACGTGATCTAGTGAGAGAGGCAGAGAAGGTGTATTACAGAAGGGAGACAGAAGAGGAGAAGGAACAGAGAAAAGAAAAGGAGAGAGAAGAAAGGGAGGAAAGACGTGATAGACGGCAAGAGAAGAATTTGACTAAGATCTTGGCCGCAGTGGTTGAAGGGAAGAGCAGCAGGGAGAGAGAGAGAGATTTTAGGAAAATTAGGTCA------GGCCCTAGACAGTCAGGGAACCTGGGCAATAGGACCCCACTCGACAAGGACCAATGTGCGTATTGTAAAGAAAAAGGACACTGGGCAAGGAACTGCCCCAAGAAGGGAAAC---AAAGGACCGAAGGTCCTAGCTCTAGAAGAAGATAAAGATTAGGGGAGACGGGGTTCGGACCCCCTCCCCGAGCCCAGGGTAACTTTGAAGGTGGAGGGTCAACACAGTGATGGGTTTGTTAA.............................AACCATTAGGAAAACTAAAAGAAAAAAAATCCTGGGTGATGGGTGCCACAGGGCAACGGCAGTATCCATGGACTACCCGAAGAACCGTTGACTTGGGAGTGGGACGGGTAACCCACTCGTTTCTGGTCATCCCTGAGTGCCCAGTACCCCTTCTAGGTAGAGACTTACTGACCAAGATGGGAGCTCAAATTTCTTTTGAACAAGGAAGACCAGAAGTGTCTGTGAATAACAAACCCATCACTGTGTTGACCCTCCAATTAGATGATGAATATCGACTATATTCTCCCCAAGTAAAGCCTGATCAAGATATACAGTCCTGGTTGGAGCAGTTTCCCCAAGCC

TGGGCAGAAACCGCAGGGATGGGTTTGGCAAAGCAAGTTCCCCCACAGGTTATTCAACTGAAGGCCAGTGCTACACCAGTATCAGTCAGACAGTACCCCTTGAGTAGAGAGGCTCGAGAAGGAATTTGGCCGCATGTTCAAAGATTAATCCAACAGGGCATCCTAGTTCCTGTCCAATCCCCTTGGAATACTCCCCTGCTACCGGTTAGGAAGCCTGGGACCAATGATTATCGACCAGTACAGGACTTGAGAGAGGTCAATAAAAGGGTGCAGGACATACACCCAACGGTCCCGAACCCTTATAACCTCTTGAGCGCCCTCCCGCCTGAACGGAACTGGTACACAGTATTGGACTTAAAAGATGCCTTCTTCTGCCTGAGATTACACCCCACTAGCCAACCACTTTTTGCCTTCGAATGGAGAGATCCAGGTACGGGAAGAACCGGGCAGCTCACCTGGACCCGACTGCCCCAAGGGTTCAAGAACTCCCCGACCATCTTTGACGAAGCCCTACACAGGGACCTGGCCAACTTCAGGATCCAACACCCTCAGGTGACCCTCCTCCAGTACGTGGATGACCTGCTTCTGGCGGGAGCCACCAAACAGGACTGCTTAGAAGGTACGAAGGCACTACTGCTGGAATTGTCTGACCTAGGCTACAGAGCCTCTGCTAAGAAGGCCCAGATTTGCAGGAGAGAGGTAACATACTTGGGGTACAGTTTGCGGGGCGGGCAGCGATGGCTGACGGAGGCACGGAAGGCCAC............................................................................................................................................................................................................................................

100

200

300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

1600

1700

1800

1900

2000

2100

2200

2300

2400

2500

2600

2700

2800

2900

3000

3100

3200

3300

3400

3500

3600

3700

3800

3900

4000

4100

4200

4300

4400

4500

4600

4700

4800

4900

5000

5100

5200

5300

5400

5500

5600

5700

5800

5900

6000

6100

6200

6300

6400

6500

6600

6700

6800

6900

7000

7100

7200

7300

7400

7500

7600

7700

7800

7900

8000

8100

8200

8300

8400

gag

MGQGESTPLSLTLDHWKDVKTRAHNLSVEIRKGKWQTFCSSEWPTFEVGWPPEGTFNPSIISAVKRIVFQETGGHPDQVPYIIVWQDLSNSPPPWVPPLAKIAVASGQDNGRKSAGGRPSAPSRLPIYPETDSLFLLSEPPPYPTSPPPPPAPHAARPAPGLMAEGLGSEGPAAGTRSRRPRSPTGDTGPDSTVALPLRAVGPPAEPNGLVPLQYWPFSSADLYNWKSNHPSFSENPTGLTGLLESLMFSHQPTWDDCQQLLQVLFTTEERERILLEARKNVLGVNGAPTQLENLINEAFPLNRPQWDHNTAEGRERLLVYRRTLVAGLKGAARRPTNLAKVREVLQGPTEPPSVFLERLMEAYRRYTPFDPSSEGQKAAVAMSFIGQSAPDIKKKLQRLEGLQDHSLQDLIKEAEKVYHKRETEEEKQEREKKETEERERRRDRRQEKNLTKILAAVVSEKGFRGRQAGNLSNRAMRAPREG-----RPPLDKDQCAYCKERGHWARECPRKKNARETNVLTLG---D*

....................................................................................................................................................................................................................WRYWPFSSADLYNWKTNHPPFSEDPQRLTGLVESLMFSHQPTWDDCQQLLQTLFTTEERERILLEARKNVPGADGRPTQLQNEIDMGFPLTRPGWDYNTAEGRESLKIYRQALVAGLRGASRRPTNLAKVREVMQGPNEPPSVFLERLMEAFRRFTPFDPTSEAQKASVALAFIGQSALDIRKKLQRLEGLQEAELRDLVREAEKVYYRRETEEEKEQRKEKEREEREERRDRRQEKNLTKILAAVVEGKSSRERERDFRKIRS--GPRQSGNLGNRTPLDKDQCAYCKEKGHWARNCPKKGN-KGPKVLALEEDKD*

pol

MGKMGSKRTVVAGATGSKVYPWTTKRLLKIGQKQVTHSFLVIPECPAPLLGRDLLTKLKAQIQFSTEGPQVTWEDRPAMCLVLNLEEEYRLHEKPVPPSID-PSWLQLFPMVWAEKAGMGLANQVPPVVVELKSDASPVAVRQYPMSKEAREGIRPHIQRFLDLGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSSLPPSHTWYSVLDLKDAFFCLKLHPNSQPLFAFEWRDPEKGNTGQLTWTRLPQGFKNSPTLFDEALHRDLASFRALNPQVVMLQYVDDLLVAAPTYRDCKEGTRRLLQELSKLGYRVSAKKAQLCREEVTYLGYLLKGGKRWLTPARKATVMKIPTPTTPRQVREFLGTAGFCRLWIPGFASLAAPLYPLTREKVPFTWTEAHQEAFGRIKEALLSAPALALPDLTKPFALYVDEKEGVARGVLTQTLGPWRRPVAYLSKKLDPVASGWPTCLKAIAAVALLLKDADKLTLGQNVLVIAPHNLESIVRQPPDRWMTNARMTHYQSLLLNERVSFAPPAILNPATLLPVESDDTPIHICSEILAEETGTRPDLRDQPLPGVPAWYTDGSSFIMDGRRQAGAAIVDNKRTVWASNLPEGTSAQKAELIALTQALRLAEGKSINIYTDSRYAFATAHVHGAIYKQRGLLTSAGKDIKNKEEILALLEAIHLPKRVAIIHCPGHQRGTDPVATGNRKADEAAKQAAQSTRILTETTKNQEHFEPTRGKIKPRELTPDQGREFIQRLHQLTHLGPDKLLQLVGRTSFHIPNLQSVVREITSKCQVCAVTNAVTTYREPGRRQRGDRPGVYWEVDFTEVKPGRYGNRYLLVFIDTFSGWVEAFPTKTETALTVCKKILEEILPRFGIPKVLGSDNGPAFVAQVSQGLATQLGIDWKLHCAYRPQSSGQVERMNRTIKETLTKLALETGGKDWVTLLPLALLRARNTPGQFGLTPYEILHGGPPPVLASG

LGKLKEKKSWVMGATGQRQYPWTTRRTVDLGVGRVTHSFLVIPECPVPLLGRDLLTKMGAQISFEQGRPEVSVNNKPITVLTLQLDDEYRLYSPQVKPDQDIQSWLEQFPQAWAETAGMGLAKQVPPQVIQLKASATPVSVRQYPLSREAREGIWPHVQRLIQQGILVPVQSPWNTPLLPVRKPGTNDYRPVQDLREVNKRVQDIHPTVPNPYNLLSALPPERNWYTVLDLKDAFFCLRLHPTSQPLFAFEWRDPGTGRTGQLTWTRLPQGFKNSPTIFDEALHRDLANFRIQHPQVTLLQYVDDLLLAGATKQDCLEGTKALLLELSDLGYRASAKKAQICRREVTYLGYSLRGGQRWLTEARKAX.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

EVVGSNGDFFPVLFTHLKALEVVRTQIWDQIKEAYRPGTVAIPHPFQVGDRVLVRRHRSGSLEPRWKGPYLVLLTTPTAVKVDGIAAWVHASHLKPAPPGAPDESWELEKTDHPLKLRVRRRRNESTA*

.................................................................................................................................

env

MLLISNPRHLGHPMSPGNWKRLIILLSCVFGGAEMNQQHNNPHQPMTLTWQVLSQTGSVVWEKKAVEPPWTWWPSLEPDVCALVAGLESWDIPELTASASQQARPPDSNYEHAYNQITWGTLGCSYPRARTRIARSQFYVCPRDGRSLSEARRCGGLESLYCKEWGCETAGTAYWQPRSSWDLITVGQGHPTGTCERTGWCNPLKIEFTEPGKRFRNWLQGRTWGLRFYVTGHPGVQLTIRLVITSPPPVVVGPDPVLAEQGPPRKIPFLPRVPVPTLSPPASPIPTVQASPPAPSTPSPTTGDRLFGLVQGAFLALNATNPEATESCWLCLALGPPYYEGIATPGQVTYASTDSQCRWGGKGKLTLTEVSGLGLCIGKVPPTHQHLCNLTIPLNASHTHKYLLPSNRSWWACNSGLTPCLSTSVFNQSNDFCIQIQLVPRIYYHPDGTLLQAYESPHSRNKREPVSLTLAVLLGLGVAAGIGTGSTALIKGPIDLQQGLTSLQIAMDTDLRALQDSISKLEDSLTSLSEVVLQNRRGLDLLFLKEGGLCAALKEECCFYVDHSGAVRDSMRRLKERLDKRQLEHQKNLSWYEGWFNRSPWLTTLLSALAGPLLLLLLLLTLGPCVINKLVQFINDRVSAVRILVLRHKYQTLDNEDNL*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	1597	3737	25.1%	1417	33.9%	2103 (98.3%)	1426 (66.7%)	27/9
Mutations:	1598T>G 1601A>G 1602A>G 1611T>C 1614C>T 1617C>T 1620A>T 1642T>A 1647T>C 1653T>C 1654T>C 1659T>C 1662C>G 1666A>G 1671T>C 1672A>C 1673C>A 1675G>C 1677A>C 1680T>C 1686A>G 1687C>T 1689C>G 1690C>G 1692T>G 1701C>T 1707T>C 1710C>T 1728C>T 1734C>T 1737G>A 1743C>G 1749A>G 1750G>A 1751T>C 1752C>A 1758T>C 1761C>A 1770A>G 1771A>C 1776A>G 1779G>A 1785T>G 1788G>A 1795C>A 1797C>A 1803C>T 1806C>T 1808T>C 1812A>G 1814T>C 1815T>C 1816A>G 1822G>C 1823C>G 1824C>A 1827T>C 1830A>G 1833A>G 1834C>T 1836C>G 1837G>C 1839G>A 1842C>T 1843C>G 1844T>A 1845C>G 1849A>G 1851T>C 1852G>A 1853A>T 1856C>G 1857C>A 1860C>T 1864C>T 1866T>G 1868A>C 1872A>C 1875T>C 1876C>G 1877A>G 1878G>T 1884T>C 1885C>T 1909C>A 1911T>C 1912C>T 1914C>G 1915C>A 1916T>A 1917G>A 1918G>A 1923C>T 1928G>A 1930A>G 1935A>G 1948A>C 1949A>G 1950A>G 1953G>C 1956A>C 1957G>T 1962G>A 1965C>G 1971C>T 1980C>T 1992A>G 1995C>G 1996T>A 2007A>G 2009C>A 2010A>C 2016C>T 2019G>C 2022C>G 2025T>A 2031A>T 2034A>G 2035C>A 2037T>G 2040A>C 2046G>A 2049T>C 2051A>T 2052T>C 2056A>C 2058A>G 2060A>T 2061T>C 2067A>T 2076C>T 2077T>A 2079T>C 2082T>A 2087G>C 2088A>C 2091A>G 2094G>A 2097G>C 2098G>T 2100G>A 2107A>C 2110T>G 2115T>C 2118C>T 2127T>G 2130C>T 2132C>T 2139T>C 2141A>G 2142A>G 2149T>C 2151A>T 2154A>G 2157G>A 2166A>G 2167C>T 2169C>A 2175C>G 2176C>G 2177A>C 2179T>G 2180C>A 2181C>G 2184G>A 2186A>G 2187G>T 2193C>A 2194A>G 2196A>G 2198A>G 2199G>A 2214A>G 2218C>T 2220T>C 2222A>G 2223G>A 2226A>G 2235G>A 2238A>G 2241A>G 2245C>G 2248G>C 2250A>G 2254G>A 2256G>A 2257A>G 2267C>G 2271G>A 2277A>G 2281A>G 2282G>A 2284C>A 2286G>A 2292C>T 2295G>A 2298C>G 2301G>A 2307A>G 2310C>T 2316C>T 2319A>G 2331G>A 2334A>G 2337A>T 2338A>G 2339G>A 2340T>A 2342A>G 2346A>G 2347G>A 2349G>C 2350T>A 2351T>G 2355A>G 2357G>A 2362C>G 2365G>A 2366C>G 2369G>A 2370G>T 2371A>T 2372A>T 2374C>A 2375T>G 2378G>A 2379C>A 2381A>T 2382C>T 2386G>T 2389_2394delATGAGG 2396C>G 2397A>C 2403G>A 2404G>C 2406A>G 2407G>T 2408G>C 2409_2410insGGGAACCTGGGCAAT 2412A>G 2413C>A 2415G>C 2418T>A 2421G>C 2427A>G 2430T>C 2433G>A 2436C>T 2439A>G 2442C>T 2453G>A 2454G>A 2457C>A 2460T>C 2470G>A 2472G>C 2479C>A 2480G>A 2485A>G 2486A>G 2487G>A 2491_2493delGCC 2495G>A 2496G>A 2498A>G 2500A>C 2502C>G 2505T>G 2511G>A 2512A>G 2514C>T 2517G>A 2519G>A 2520T>A 2520_2521insGAAGATAAA 2523C>T 2532T>A 2568G>T 2571A>G 2573C>A 2574T>G 2583G>T 2584A>C 2585T>A 2586C>A 2588C>A 2591C>G 2595G>T 2596T>G 2597T>G 2598T>G 2601G>T 2605G>A 2637G>A 2640T>A 2641A>T 2643G>A 2649G>A 2650A>C 2652G>A 2653G>A 2654G>A 2656T>G 2657C>A 2658C>A 2662C>A 2663G>A 2664G>A 2665A>T 2667A>C 2668G>T 2669T>G 2670C>G 2674G>A 2675C>T 2676T>G 2679G>T 2682G>C 2685G>A 2688C>G 2689A>C 2690G>A 2691C>A 2692A>C 2693A>G 2694A>G 2695G>C 2696T>A 2697T>G 2700C>T 2703T>A 2709C>T 2713A>C 2714A>G 2715G>A 2719C>A 2720T>C 2721T>C 2722T>G 2724G>T 2725A>G 2727A>C 2728A>T 2730T>G 2734C>G 2735A>T 2736A>G 2737A>G 2738A>G 2739G>A 2741A>G 2742A>G 2745G>A 2754A>G 2757C>T 2758T>C 2766A>C 2769C>T 2772A>G 2778T>A 2780C>T 2781T>A 2787G>T 2788T>C 2793C>T 2796G>A 2800C>T 2802C>A 2805C>G 2812C>A 2814A>G 2815A>G 2816A>G 2826C>T 2827C>T 2828A>C 2829G>T 2833T>G 2834C>A 2835C>A 2836A>C 2837C>A 2840A>G 2841G>A 2842G>A 2844C>A 2848C>G 2850G>A 2853A>G 2854A>T 2856A>T 2857T>G 2858G>T 2860G>A 2862A>T 2863G>A 2866C>A 2867G>A 2868C>A 2872G>A 2873C>T 2876T>C 2877G>T 2878T>G 2879G>T 2880T>G 2883A>G 2884G>A 2885T>C 2889G>C 2890A>C 2892C>A 2895G>A 2898G>T 2901G>T 2907C>T 2911T>C 2914C>T 2916C>T 2917G>T 2918A>C 2919A>T 2920A>C 2921A>C 2922G>C 2924C>A 2925G>A 2928C>A 2929C>A 2930C>A 2931T>G 2935T>G 2936C>A 2938A>C 2939T>A 2940C>A 2943C>T 2943_2944insATA 2945C>A 2949A>C 2953C>T 2955C>G 2956C>G 2958A>G 2960T>A 2961C>G 2968A>C 2969T>A 2970G>A 2972T>C 2973T>C 2979C>A 2982G>A 2984A>C 2985G>C 2991T>G 2997A>T 2998C>T 3003C>A 3006T>G 3012C>T 3015A>C 3019G>C 3020T>A 3024A>T 3025G>A 3027G>T 3028G>C 3037T>G 3039A>C 3040G>A 3041A>G 3045C>T 3046T>A 3054G>A 3055G>T 3057T>A 3060T>C 3061C>A 3072A>C 3073A>T 3078C>T 3080A>G 3081G>A 3084A>G 3087C>T 3090G>A 3093G>A 3096T>A 3099C>T 3100A>T 3105C>G 3108C>T 3109A>G 3111C>T 3120C>A 3121T>A 3123G>C 3124G>C 3126T>A 3127T>C 3128T>A 3132G>C 3135T>C 3138G>A 3141A>T 3145T>G 3146G>T 3150G>A 3153G>C 3156C>T 3162C>T 3165C>T 3168T>C 3169T>C 3172T>C 3177T>G 3180A>T 3182A>G 3183A>G 3186A>G 3192A>G 3201C>T 3207G>A 3213C>A 3216A>G 3219T>C 3225G>A 3234C>T 3240A>G 3243A>G 3252T>A 3255T>C 3258C>A 3261A>G 3273C>T 3282A>C 3283C>T 3285C>G 3288T>C 3289T>G 3300C>T 3301A>G 3302G>A 3303C>A 3305A>G 3306C>G 3308C>A 3315T>C 3316T>A 3321T>A 3324A>G 3328C>T 3330C>A 3339T>C 3345T>C 3351C>G 3353A>G 3354G>A 3355C>T 3365A>C 3366C>T 3372G>A 3376T>C 3378G>T 3381C>T 3384G>C 3387T>C 3404A>G 3405A>T 3407A>C 3408A>G 3411C>A 3413A>G 3414T>A 3417T>C 3420C>G 3426A>C 3435T>C 3438G>A 3441A>G 3444G>C 3450A>G 3462T>C 3465C>G 3469C>A 3474C>T 3477T>C 3480G>A 3486C>A 3490C>A 3495T>C 3501A>C 3502T>A 3503C>A 3511G>A 3512C>T 3513T>C 3515T>A 3516C>A 3517A>C 3522C>T 3528A>G 3529G>A 3530T>C 3531G>C 3532A>C 3534G>C 3540A>G 3543T>C 3546T>G 3555C>G 3558G>T 3559G>C 3561A>G 3566C>G 3567C>A 3568C>G 3570A>C 3573G>C 3574T>A 3576C>A 3578G>A 3579A>G 3586A>T 3587A>T 3594G>T 3597A>G 3598C>A 3599G>A 3600A>G 3601A>G 3602G>C 3603G>A 3606C>A 3607T>C 3609A>G 3611A>T 3616C>T 3618A>G 3619A>T 3620G>C 3622A>G 3624G>C 3625T>C 3627G>A 3630A>C 3634C>A 3638T>C 3639G>C 3642G>T 3645C>T 3648A>G 3658C>A 3664C>A 3667G>A 3668A>G 3669G>A 3672A>G 3675T>A 3678G>A 3681T>C 3682C>T 3684C>G 3690T>C 3691T>A 3692T>G 3693G>T 3694C>T 3696A>G 3697A>C 3698A>G 3699A>G 3702G>C 3706A>C 3709A>C 3720C>G 3721C>G 3722C>A 3723A>G 3726C>A 3729A>G
CDS

gag	213	522	59.4%	1605	75.8%	307 (96.5%)	227 (71.4%)	8/3/0/0	1
Protein mutations:	L213W (1598T>G) Q214R (1601A>G 1602A>G) S228T (1642T>A) S232P (1654T>C) N236D (1666A>G) T238Q (1672A>C 1673C>A) G239R (1675G>C 1677A>C) L244V (1690C>G 1692T>G) V264T (1750G>A 1751T>C 1752C>A) L283P (1808T>C) V285A (1814T>C 1815T>C) N286D (1816A>G) A288R (1822G>C 1823C>G 1824C>A) E293Q (1837G>C 1839G>A) L295E (1843C>G 1844T>A 1845C>G) N297D (1849A>G 1851T>C) E298M (1852G>A 1853A>T) A299G (1856C>G 1857C>A) N303T (1868A>C) Q306G (1876C>G 1877A>G 1878G>T) H309Y (1885C>T) R317S (1909C>A 1911T>C) L319K (1915C>A 1916T>A 1917G>A) V320I (1918G>A) R323Q (1928G>A) T324A (1930A>G) K330R (1948A>C 1949A>G 1950A>G) A333S (1957G>T) L346M (1996T>A) T350N (2009C>A 2010A>C) Y364F (2051A>T 2052T>C) Y367F (2060A>T 2061T>C) S373T (2077T>A 2079T>C) G376A (2087G>C 2088A>C) A380S (2098G>T 2100G>A) M383L (2107A>C) S384A (2110T>G) P391L (2132C>T) K394R (2141A>G 2142A>G) D405E (2175C>G) H406A (2176C>G 2177A>C) S407E (2179T>G 2180C>A 2181C>G) Q409R (2186A>G 2187G>T) I412V (2194A>G 2196A>G) K413R (2198A>G 2199G>A) H420Y (2218C>T 2220T>C) K421R (2222A>G 2223G>A) Q429E (2245C>G) E430Q (2248G>C 2250A>G) E432K (2254G>A 2256G>A) K433E (2257A>G) T436R (2267C>G) R441E (2281A>G 2282G>A) S460E (2338A>G 2339G>A 2340T>A) E461G (2342A>G) G463S (2347G>A 2349G>C) F464S (2350T>A 2351T>G) G466E (2357G>A) Q468E (2362C>G) A469R (2365G>A 2366C>G) G470D (2369G>A 2370G>T) N471F (2371A>T 2372A>T) L472R (2374C>A 2375T>G) S473K (2378G>A 2379C>A) N474I (2381A>T 2382C>T) A476S (2386G>T) M477_R478del (2389_2394delATGAGG) A479G (2396C>G 2397A>C) E482Q (2404G>C 2406A>G) G483S (2407G>T 2408G>C) G483_R484insGNLGN (2409_2410insGGGAACCTGGGCAAT) P485T (2413C>A 2415G>C) R498K (2453G>A 2454G>A) E504N (2470G>A 2472G>C) R507K (2479C>A 2480G>A) K509G (2485A>G 2486A>G 2487G>A) A511del (2491_2493delGCC) R512K (2495G>A 2496G>A) E513G (2498A>G) T514P (2500A>C 2502C>G) N515K (2505T>G) T518A (2512A>G 2514C>T) G520E (2519G>A 2520T>A) G520_D521insEDK (2520_2521insGAAGATAAA)
Codon mutations:	TTG213TGG (1598T>G) CAA214CGG (1601A>G 1602A>G) CCT217CCC (1611T>C) TTC218TTT (1614C>T) TCC219TCT (1617C>T) TCA220TCT (1620A>T) TCT228ACT (1642T>A) AAT229AAC (1647T>C) CCT231CCC (1653T>C) TCT232CCT (1654T>C) TTT233TTC (1659T>C) TCC234TCG (1662C>G) AAT236GAT (1666A>G) CCT237CCC (1671T>C) ACA238CAA (1672A>C 1673C>A) GGA239CGC (1675G>C 1677A>C) CTT240CTC (1680T>C) GGA242GGG (1686A>G) CTC243TTG (1687C>T 1689C>G) CTT244GTG (1690C>G 1692T>G) CTC247CTT (1701C>T) TTT249TTC (1707T>C) TCC250TCT (1710C>T) GAC256GAT (1728C>T) TGC258TGT (1734C>T) CAG259CAA (1737G>A) CTC261CTG (1743C>G) CAA263CAG (1749A>G) GTC264ACA (1750G>A 1751T>C 1752C>A) TTT266TTC (1758T>C) ACC267ACA (1761C>A) GAA270GAG (1770A>G) AGA271CGA (1771A>C) GAA272GAG (1776A>G) AGG273AGA (1779G>A) CTT275CTG (1785T>G) TTG276TTA (1788G>A) CGC279AGA (1795C>A 1797C>A) AAC281AAT (1803C>T) GTC282GTT (1806C>T) CTT283CCT (1808T>C) GGA284GGG (1812A>G) GTT285GCC (1814T>C 1815T>C) AAC286GAC (1816A>G) GCC288CGA (1822G>C 1823C>G 1824C>A) CCT289CCC (1827T>C) ACA290ACG (1830A>G) CAA291CAG (1833A>G) CTC292TTG (1834C>T 1836C>G) GAG293CAA (1837G>C 1839G>A) AAC294AAT (1842C>T) CTC295GAG (1843C>G 1844T>A 1845C>G) AAT297GAC (1849A>G 1851T>C) GAG298ATG (1852G>A 1853A>T) GCC299GGA (1856C>G 1857C>A) TTC300TTT (1860C>T) CTT302TTG (1864C>T 1866T>G) AAT303ACT (1868A>C) CGA304CGC (1872A>C) CCT305CCC (1875T>C) CAG306GGT (1876C>G 1877A>G 1878G>T) GAT308GAC (1884T>C) CAC309TAC (1885C>T) CGT317AGC (1909C>A 1911T>C) CTC318TTG (1912C>T 1914C>G) CTG319AAA (1915C>A 1916T>A 1917G>A) GTC320ATC (1918G>A) TAC321TAT (1923C>T) CGG323CAG (1928G>A) ACT324GCT (1930A>G) CTA325CTG (1935A>G) AAA330CGG (1948A>C 1949A>G 1950A>G) GGG331GGC (1953G>C) GCA332GCC (1956A>C) GCA333TCA (1957G>T) AGG334AGA (1962G>A) CGC335CGG (1965C>G) ACC337ACT (1971C>T) GCC340GCT (1980C>T) GAA344GAG (1992A>G) GTC345GTG (1995C>G) TTG346ATG (1996T>A) CCA349CCG (2007A>G) ACA350AAC (2009C>A 2010A>C) CCC352CCT (2016C>T) CCG353CCC (2019G>C) TCC354TCG (2022C>G) GTT355GTA (2025T>A) CTA357CTT (2031A>T) GAA358GAG (2034A>G) CGT359AGG (2035C>A 2037T>G) CTA360CTC (2040A>C) GAG362GAA (2046G>A) GCT363GCC (2049T>C) TAT364TTC (2051A>T 2052T>C) AGA366CGG (2056A>C 2058A>G) TAT367TTC (2060A>T 2061T>C) CCA369CCT (2067A>T) CCC372CCT (2076C>T) TCT373ACC (2077T>A 2079T>C) TCT374TCA (2082T>A) GGA376GCC (2087G>C 2088A>C) CAA377CAG (2091A>G) AAG378AAA (2094G>A) GCG379GCC (2097G>C) GCG380TCA (2098G>T 2100G>A) ATG383CTG (2107A>C) TCC384GCC (2110T>G) TTT385TTC (2115T>C) ATC386ATT (2118C>T) TCT389TCG (2127T>G) GCC390GCT (2130C>T) CCG391CTG (2132C>T) ATT393ATC (2139T>C) AAA394AGG (2141A>G 2142A>G) TTA397CTT (2149T>C 2151A>T) CAA398CAG (2154A>G) AGG399AGA (2157G>A) GGA402GGG (2166A>G) CTC403TTA (2167C>T 2169C>A) GAC405GAG (2175C>G) CAT406GCT (2176C>G 2177A>C) TCC407GAG (2179T>G 2180C>A 2181C>G) TTG408TTA (2184G>A) CAG409CGT (2186A>G 2187G>T) CTC411CTA (2193C>A) ATA412GTG (2194A>G 2196A>G) AAG413AGA (2198A>G 2199G>A) GTA418GTG (2214A>G) CAT420TAC (2218C>T 2220T>C) AAG421AGA (2222A>G 2223G>A) AGA422AGG (2226A>G) GAG425GAA (2235G>A) GAA426GAG (2238A>G) GAA427GAG (2241A>G) CAA429GAA (2245C>G) GAA430CAG (2248G>C 2250A>G) GAG432AAA (2254G>A 2256G>A) AAA433GAA (2257A>G) ACA436AGA (2267C>G) GAG437GAA (2271G>A) AGA439AGG (2277A>G) AGA441GAA (2281A>G 2282G>A) CGG442AGA (2284C>A 2286G>A) GAC444GAT (2292C>T) AGG445AGA (2295G>A) CGC446CGG (2298C>G) CAG447CAA (2301G>A) AAA449AAG (2307A>G) AAC450AAT (2310C>T) ACC452ACT (2316C>T) AAA453AAG (2319A>G) GCG457GCA (2331G>A) GTA458GTG (2334A>G) GTA459GTT (2337A>T) AGT460GAA (2338A>G 2339G>A 2340T>A) GAG461GGG (2342A>G) AAA462AAG (2346A>G) GGG463AGC (2347G>A 2349G>C) TTC464AGC (2350T>A 2351T>G) AGA465AGG (2355A>G) GGG466GAG (2357G>A) CAG468GAG (2362C>G) GCA469AGA (2365G>A 2366C>G) GGG470GAT (2369G>A 2370G>T) AAT471TTT (2371A>T 2372A>T) CTG472AGG (2374C>A 2375T>G) AGC473AAA (2378G>A 2379C>A) AAC474ATT (2381A>T 2382C>T) GCA476TCA (2386G>T) ATG477_AGG478del (2389_2394delATGAGG) GCA479GGC (2396C>G 2397A>C) AGG481AGA (2403G>A) GAA482CAG (2404G>C 2406A>G) GGA483TCA (2407G>T 2408G>C) GGA483_AGA484insGGGAACCTGGGCAAT (2409_2410insGGGAACCTGGGCAAT) AGA484AGG (2412A>G) CCG485ACC (2413C>A 2415G>C) CCT486CCA (2418T>A) CTG487CTC (2421G>C) AAA489AAG (2427A>G) GAT490GAC (2430T>C) CAG491CAA (2433G>A) TGC492TGT (2436C>T) GCA493GCG (2439A>G) TAC494TAT (2442C>T) AGG498AAA (2453G>A 2454G>A) GGC499GGA (2457C>A) CAT500CAC (2460T>C) GAG504AAC (2470G>A 2472G>C) CGG507AAG (2479C>A 2480G>A) AAG509GGA (2485A>G 2486A>G 2487G>A) GCC511del (2491_2493delGCC) AGG512AAA (2495G>A 2496G>A) GAA513GGA (2498A>G) ACC514CCG (2500A>C 2502C>G) AAT515AAG (2505T>G) CTG517CTA (2511G>A) ACC518GCT (2512A>G 2514C>T) CTG519CTA (2517G>A) GGT520GAA (2519G>A 2520T>A) GGT520_GAC521insGAAGATAAA (2520_2521insGAAGATAAA) GAC521GAT (2523C>T)
pol	1	366	32.4%	1952	74.8%	366 (99.7%)	260 (70.8%)	1/0/0/0	0
Protein mutations:	M1L (2641A>T 2643G>A) M4L (2650A>C 2652G>A) G5K (2653G>A 2654G>A) S6E (2656T>G 2657C>A 2658C>A) R8K (2662C>A 2663G>A 2664G>A) T9S (2665A>T 2667A>C) V10W (2668G>T 2669T>G 2670C>G) A12M (2674G>A 2675C>T 2676T>G) S17Q (2689A>C 2690G>A 2691C>A) K18R (2692A>C 2693A>G 2694A>G) V19Q (2695G>C 2696T>A 2697T>G) K25R (2713A>C 2714A>G 2715G>A) L27T (2719C>A 2720T>C 2721T>C) L28V (2722T>G 2724G>T) K29D (2725A>G 2727A>C) I30L (2728A>T 2730T>G) Q32V (2734C>G 2735A>T 2736A>G) K33G (2737A>G 2738A>G 2739G>A) Q34R (2741A>G 2742A>G) A47V (2780C>T 2781T>A) L58M (2812C>A 2814A>G) K59G (2815A>G 2816A>G) Q63S (2827C>T 2828A>C 2829G>T) S65E (2833T>G 2834C>A 2835C>A) T66Q (2836A>C 2837C>A) E67G (2840A>G 2841G>A) G68R (2842G>A 2844C>A) Q70E (2848C>G 2850G>A) T72S (2854A>T 2856A>T) W73V (2857T>G 2858G>T) E74N (2860G>A 2862A>T) D75N (2863G>A) R76K (2866C>A 2867G>A 2868C>A) A78I (2872G>A 2873C>T) M79T (2876T>C 2877G>T) C80V (2878T>G 2879G>T 2880T>G) V82T (2884G>A 2885T>C) N84Q (2890A>C 2892C>A) E86D (2898G>T) E87D (2901G>T) H92Y (2914C>T 2916C>T) E93S (2917G>T 2918A>C 2919A>T) K94P (2920A>C 2921A>C 2922G>C) P95Q (2924C>A 2925G>A) P97K (2929C>A 2930C>A 2931T>G) S99D (2935T>G 2936C>A) I100Q (2938A>C 2939T>A 2940C>A) D101_P102insI (2943_2944insATA) P102Q (2945C>A) Q106E (2956C>G 2958A>G) L107Q (2960T>A 2961C>G) M110Q (2968A>C 2969T>A 2970G>A) V111A (2972T>C 2973T>C) K115T (2984A>C 2985G>C) N122K (3006T>G) V127Q (3019G>C 3020T>A) V129I (3025G>A 3027G>T) E130Q (3028G>C) S133A (3037T>G 3039A>C) D134S (3040G>A 3041A>G) S136T (3046T>A) A139S (3055G>T 3057T>A) M145L (3073A>T) K147R (3080A>G 3081G>A) R154W (3100A>T) I157V (3109A>G 3111C>T) F160L (3120C>A) L161I (3121T>A 3123G>C) D162Q (3124G>C 3126T>A) L163Q (3127T>C 3128T>A) C169V (3145T>G 3146G>T) K181R (3182A>G 3183A>G) S217A (3289T>G) S221E (3301A>G 3302G>A 3303C>A) H222R (3305A>G 3306C>G) T223N (3308C>A) S226T (3316T>A) K238R (3353A>G 3354G>A) N242T (3365A>C 3366C>T) E255G (3404A>G 3405A>T) K256T (3407A>C 3408A>G) N258R (3413A>G 3414T>A) L277I (3469C>A) S288N (3502T>A 3503C>A) A291I (3511G>A 3512C>T 3513T>C) L292Q (3515T>A 3516C>A) N293H (3517A>C) V297T (3529G>A 3530T>C 3531G>C) M298L (3532A>C 3534G>C) V307L (3559G>C 3561A>G) A309G (3566C>G 3567C>A) P310A (3568C>G 3570A>C) Y312K (3574T>A 3576C>A) R313Q (3578G>A 3579A>G) K316L (3586A>T 3587A>T) R320K (3598C>A 3599G>A 3600A>G) R321A (3601A>G 3602G>C 3603G>A) Q324L (3611A>T) K328D (3622A>G 3624G>C) V333A (3638T>C 3639G>C) L340I (3658C>A) E343R (3667G>A 3668A>G 3669G>A) L351S (3691T>A 3692T>G 3693G>T) K353R (3697A>C 3698A>G 3699A>G) K356Q (3706A>C) P361E (3721C>G 3722C>A 3723A>G)
Codon mutations:	ATG1TTA (2641A>T 2643G>A) AAG3AAA (2649G>A) ATG4CTA (2650A>C 2652G>A) GGA5AAA (2653G>A 2654G>A) TCC6GAA (2656T>G 2657C>A 2658C>A) CGG8AAA (2662C>A 2663G>A 2664G>A) ACA9TCC (2665A>T 2667A>C) GTC10TGG (2668G>T 2669T>G 2670C>G) GCT12ATG (2674G>A 2675C>T 2676T>G) GGG13GGT (2679G>T) GCG14GCC (2682G>C) ACG15ACA (2685G>A) GGC16GGG (2688C>G) AGC17CAA (2689A>C 2690G>A 2691C>A) AAA18CGG (2692A>C 2693A>G 2694A>G) GTT19CAG (2695G>C 2696T>A 2697T>G) TAC20TAT (2700C>T) CCT21CCA (2703T>A) ACC23ACT (2709C>T) AAG25CGA (2713A>C 2714A>G 2715G>A) CTT27ACC (2719C>A 2720T>C 2721T>C) TTG28GTT (2722T>G 2724G>T) AAA29GAC (2725A>G 2727A>C) ATT30TTG (2728A>T 2730T>G) CAA32GTG (2734C>G 2735A>T 2736A>G) AAG33GGA (2737A>G 2738A>G 2739G>A) CAA34CGG (2741A>G 2742A>G) GTG35GTA (2745G>A) TCA38TCG (2754A>G) TTC39TTT (2757C>T) TTG40CTG (2758T>C) ATA42ATC (2766A>C) CCC43CCT (2769C>T) GAA44GAG (2772A>G) CCT46CCA (2778T>A) GCT47GTA (2780C>T 2781T>A) CTG49CTT (2787G>T) TTA50CTA (2788T>C) GGC51GGT (2793C>T) AGG52AGA (2796G>A) CTC54TTA (2800C>T 2802C>A) CTC55CTG (2805C>G) CTA58ATG (2812C>A 2814A>G) AAA59GGA (2815A>G 2816A>G) ATC62ATT (2826C>T) CAG63TCT (2827C>T 2828A>C 2829G>T) TCC65GAA (2833T>G 2834C>A 2835C>A) ACA66CAA (2836A>C 2837C>A) GAG67GGA (2840A>G 2841G>A) GGC68AGA (2842G>A 2844C>A) CAG70GAA (2848C>G 2850G>A) GTA71GTG (2853A>G) ACA72TCT (2854A>T 2856A>T) TGG73GTG (2857T>G 2858G>T) GAA74AAT (2860G>A 2862A>T) GAC75AAC (2863G>A) CGC76AAA (2866C>A 2867G>A 2868C>A) GCC78ATC (2872G>A 2873C>T) ATG79ACT (2876T>C 2877G>T) TGT80GTG (2878T>G 2879G>T 2880T>G) TTA81TTG (2883A>G) GTC82ACC (2884G>A 2885T>C) CTG83CTC (2889G>C) AAC84CAA (2890A>C 2892C>A) TTG85TTA (2895G>A) GAG86GAT (2898G>T) GAG87GAT (2901G>T) TAC89TAT (2907C>T) TTA91CTA (2911T>C) CAC92TAT (2914C>T 2916C>T) GAA93TCT (2917G>T 2918A>C 2919A>T) AAG94CCC (2920A>C 2921A>C 2922G>C) CCG95CAA (2924C>A 2925G>A) GTC96GTA (2928C>A) CCT97AAG (2929C>A 2930C>A 2931T>G) TCT99GAT (2935T>G 2936C>A) ATC100CAA (2938A>C 2939T>A 2940C>A) GAC101GAT (2943C>T) GAC101_CCG102insATA (2943_2944insATA) CCG102CAG (2945C>A) TCA103TCC (2949A>C) CTC105TTG (2953C>T 2955C>G) CAA106GAG (2956C>G 2958A>G) CTC107CAG (2960T>A 2961C>G) ATG110CAA (2968A>C 2969T>A 2970G>A) GTT111GCC (2972T>C 2973T>C) GCC113GCA (2979C>A) GAG114GAA (2982G>A) AAG115ACC (2984A>C 2985G>C) GGT117GGG (2991T>G) GGA119GGT (2997A>T) CTG120TTG (2998C>T) GCC121GCA (3003C>A) AAT122AAG (3006T>G) GTC124GTT (3012C>T) CCA125CCC (3015A>C) GTG127CAG (3019G>C 3020T>A) GTA128GTT (3024A>T) GTG129ATT (3025G>A 3027G>T) GAA130CAA (3028G>C) TCA133GCC (3037T>G 3039A>C) GAT134AGT (3040G>A 3041A>G) GCC135GCT (3045C>T) TCA136ACA (3046T>A) GTG138GTA (3054G>A) GCT139TCA (3055G>T 3057T>A) GTT140GTC (3060T>C) CGA141AGA (3061C>A) CCA144CCC (3072A>C) ATG145TTG (3073A>T) AGC146AGT (3078C>T) AAG147AGA (3080A>G 3081G>A) GAA148GAG (3084A>G) GCC149GCT (3087C>T) CGG150CGA (3090G>A) GAG151GAA (3093G>A) GGT152GGA (3096T>A) ATC153ATT (3099C>T) AGG154TGG (3100A>T) CCC155CCG (3105C>G) CAC156CAT (3108C>T) ATC157GTT (3109A>G 3111C>T) TTC160TTA (3120C>A) TTG161ATC (3121T>A 3123G>C) GAT162CAA (3124G>C 3126T>A) TTG163CAG (3127T>C 3128T>A) GGG164GGC (3132G>C) ATT165ATC (3135T>C) CTG166CTA (3138G>A) GTA167GTT (3141A>T) TGC169GTC (3145T>G 3146G>T) CAG170CAA (3150G>A) TCG171TCC (3153G>C) CCC172CCT (3156C>T) AAC174AAT (3162C>T) ACC175ACT (3165C>T) CCT176CCC (3168T>C) TTG177CTG (3169T>C) TTA178CTA (3172T>C) CCT179CCG (3177T>G) GTA180GTT (3180A>T) AAA181AGG (3182A>G 3183A>G) AAA182AAG (3186A>G) GGA184GGG (3192A>G) GAC187GAT (3201C>T) CGG189CGA (3207G>A) GTC191GTA (3213C>A) CAA192CAG (3216A>G) GAT193GAC (3219T>C) AGG195AGA (3225G>A) AAC198AAT (3234C>T) AGA200AGG (3240A>G) GTA201GTG (3243A>G) ATT204ATA (3252T>A) CAT205CAC (3255T>C) CCC206CCA (3258C>A) ACA207ACG (3261A>G) CCC211CCT (3273C>T) CTA214CTC (3282A>C) CTC215TTG (3283C>T 3285C>G) AGT216AGC (3288T>C) TCC217GCC (3289T>G) CCC220CCT (3300C>T) AGC221GAA (3301A>G 3302G>A 3303C>A) CAC222CGG (3305A>G 3306C>G) ACC223AAC (3308C>A) TAT225TAC (3315T>C) TCA226ACA (3316T>A) GTT227GTA (3321T>A) TTA228TTG (3324A>G) CTC230TTA (3328C>T 3330C>A) GCT233GCC (3339T>C) TTT235TTC (3345T>C) CTC237CTG (3351C>G) AAG238AGA (3353A>G 3354G>A) CTA239TTA (3355C>T) AAC242ACT (3365A>C 3366C>T) CAG244CAA (3372G>A) TTG246CTT (3376T>C 3378G>T) TTC247TTT (3381C>T) GCG248GCC (3384G>C) TTT249TTC (3387T>C) GAA255GGT (3404A>G 3405A>T) AAA256ACG (3407A>C 3408A>G) GGC257GGA (3411C>A) AAT258AGA (3413A>G 3414T>A) ACT259ACC (3417T>C) GGC260GGG (3420C>G) CTA262CTC (3426A>C) ACT265ACC (3435T>C) CGG266CGA (3438G>A) CTA267CTG (3441A>G) CCG268CCC (3444G>C) GGA270GGG (3450A>G) TCT274TCC (3462T>C) CCC275CCG (3465C>G) CTC277ATC (3469C>A) TTC278TTT (3474C>T) GAT279GAC (3477T>C) GAG280GAA (3480G>A) CTC282CTA (3486C>A) CGG284AGG (3490C>A) GAT285GAC (3495T>C) GCA287GCC (3501A>C) TCC288AAC (3502T>A 3503C>A) GCT291ATC (3511G>A 3512C>T 3513T>C) CTC292CAA (3515T>A 3516C>A) AAC293CAC (3517A>C) CCC294CCT (3522C>T) GTA296GTG (3528A>G) GTG297ACC (3529G>A 3530T>C 3531G>C) ATG298CTC (3532A>C 3534G>C) CAA300CAG (3540A>G) TAT301TAC (3543T>C) GTT302GTG (3546T>G) CTC305CTG (3555C>G) CTG306CTT (3558G>T) GTA307CTG (3559G>C 3561A>G) GCC309GGA (3566C>G 3567C>A) CCA310GCC (3568C>G 3570A>C) ACG311ACC (3573G>C) TAC312AAA (3574T>A 3576C>A) CGA313CAG (3578G>A 3579A>G) AAA316TTA (3586A>T 3587A>T) GGG318GGT (3594G>T) ACA319ACG (3597A>G) CGA320AAG (3598C>A 3599G>A 3600A>G) AGG321GCA (3601A>G 3602G>C 3603G>A) CTC322CTA (3606C>A) TTA323CTG (3607T>C 3609A>G) CAG324CTG (3611A>T) CTA326TTG (3616C>T 3618A>G) AGT327TCT (3619A>T 3620G>C) AAG328GAC (3622A>G 3624G>C) TTG329CTA (3625T>C 3627G>A) GGA330GGC (3630A>C) CGA332AGA (3634C>A) GTG333GCC (3638T>C 3639G>C) TCG334TCT (3642G>T) GCC335GCT (3645C>T) AAA336AAG (3648A>G) CTT340ATT (3658C>A) CGG342AGG (3664C>A) GAG343AGA (3667G>A 3668A>G 3669G>A) GAA344GAG (3672A>G) GTT345GTA (3675T>A) ACG346ACA (3678G>A) TAT347TAC (3681T>C) CTC348TTG (3682C>T 3684C>G) TAT350TAC (3690T>C) TTG351AGT (3691T>A 3692T>G 3693G>T) CTA352TTG (3694C>T 3696A>G) AAA353CGG (3697A>C 3698A>G 3699A>G) GGG354GGC (3702G>C) AAG356CAG (3706A>C) AGA357CGA (3709A>C) ACC360ACG (3720C>G) CCA361GAG (3721C>G 3722C>A 3723A>G) GCC362GCA (3726C>A) CGA363CGG (3729A>G)
Proteins

gag protein (YP_009513210.1)	213	522	59.4%	1605	75.8%	307 (96.5%)	227 (71.4%)	8/3/0/0	1
Protein mutations:	L213W (1598T>G) Q214R (1601A>G 1602A>G) S228T (1642T>A) S232P (1654T>C) N236D (1666A>G) T238Q (1672A>C 1673C>A) G239R (1675G>C 1677A>C) L244V (1690C>G 1692T>G) V264T (1750G>A 1751T>C 1752C>A) L283P (1808T>C) V285A (1814T>C 1815T>C) N286D (1816A>G) A288R (1822G>C 1823C>G 1824C>A) E293Q (1837G>C 1839G>A) L295E (1843C>G 1844T>A 1845C>G) N297D (1849A>G 1851T>C) E298M (1852G>A 1853A>T) A299G (1856C>G 1857C>A) N303T (1868A>C) Q306G (1876C>G 1877A>G 1878G>T) H309Y (1885C>T) R317S (1909C>A 1911T>C) L319K (1915C>A 1916T>A 1917G>A) V320I (1918G>A) R323Q (1928G>A) T324A (1930A>G) K330R (1948A>C 1949A>G 1950A>G) A333S (1957G>T) L346M (1996T>A) T350N (2009C>A 2010A>C) Y364F (2051A>T 2052T>C) Y367F (2060A>T 2061T>C) S373T (2077T>A 2079T>C) G376A (2087G>C 2088A>C) A380S (2098G>T 2100G>A) M383L (2107A>C) S384A (2110T>G) P391L (2132C>T) K394R (2141A>G 2142A>G) D405E (2175C>G) H406A (2176C>G 2177A>C) S407E (2179T>G 2180C>A 2181C>G) Q409R (2186A>G 2187G>T) I412V (2194A>G 2196A>G) K413R (2198A>G 2199G>A) H420Y (2218C>T 2220T>C) K421R (2222A>G 2223G>A) Q429E (2245C>G) E430Q (2248G>C 2250A>G) E432K (2254G>A 2256G>A) K433E (2257A>G) T436R (2267C>G) R441E (2281A>G 2282G>A) S460E (2338A>G 2339G>A 2340T>A) E461G (2342A>G) G463S (2347G>A 2349G>C) F464S (2350T>A 2351T>G) G466E (2357G>A) Q468E (2362C>G) A469R (2365G>A 2366C>G) G470D (2369G>A 2370G>T) N471F (2371A>T 2372A>T) L472R (2374C>A 2375T>G) S473K (2378G>A 2379C>A) N474I (2381A>T 2382C>T) A476S (2386G>T) M477_R478del (2389_2394delATGAGG) A479G (2396C>G 2397A>C) E482Q (2404G>C 2406A>G) G483S (2407G>T 2408G>C) G483_R484insGNLGN (2409_2410insGGGAACCTGGGCAAT) P485T (2413C>A 2415G>C) R498K (2453G>A 2454G>A) E504N (2470G>A 2472G>C) R507K (2479C>A 2480G>A) K509G (2485A>G 2486A>G 2487G>A) A511del (2491_2493delGCC) R512K (2495G>A 2496G>A) E513G (2498A>G) T514P (2500A>C 2502C>G) N515K (2505T>G) T518A (2512A>G 2514C>T) G520E (2519G>A 2520T>A) G520_D521insEDK (2520_2521insGAAGATAAA)
Codon mutations:	TTG213TGG (1598T>G) CAA214CGG (1601A>G 1602A>G) CCT217CCC (1611T>C) TTC218TTT (1614C>T) TCC219TCT (1617C>T) TCA220TCT (1620A>T) TCT228ACT (1642T>A) AAT229AAC (1647T>C) CCT231CCC (1653T>C) TCT232CCT (1654T>C) TTT233TTC (1659T>C) TCC234TCG (1662C>G) AAT236GAT (1666A>G) CCT237CCC (1671T>C) ACA238CAA (1672A>C 1673C>A) GGA239CGC (1675G>C 1677A>C) CTT240CTC (1680T>C) GGA242GGG (1686A>G) CTC243TTG (1687C>T 1689C>G) CTT244GTG (1690C>G 1692T>G) CTC247CTT (1701C>T) TTT249TTC (1707T>C) TCC250TCT (1710C>T) GAC256GAT (1728C>T) TGC258TGT (1734C>T) CAG259CAA (1737G>A) CTC261CTG (1743C>G) CAA263CAG (1749A>G) GTC264ACA (1750G>A 1751T>C 1752C>A) TTT266TTC (1758T>C) ACC267ACA (1761C>A) GAA270GAG (1770A>G) AGA271CGA (1771A>C) GAA272GAG (1776A>G) AGG273AGA (1779G>A) CTT275CTG (1785T>G) TTG276TTA (1788G>A) CGC279AGA (1795C>A 1797C>A) AAC281AAT (1803C>T) GTC282GTT (1806C>T) CTT283CCT (1808T>C) GGA284GGG (1812A>G) GTT285GCC (1814T>C 1815T>C) AAC286GAC (1816A>G) GCC288CGA (1822G>C 1823C>G 1824C>A) CCT289CCC (1827T>C) ACA290ACG (1830A>G) CAA291CAG (1833A>G) CTC292TTG (1834C>T 1836C>G) GAG293CAA (1837G>C 1839G>A) AAC294AAT (1842C>T) CTC295GAG (1843C>G 1844T>A 1845C>G) AAT297GAC (1849A>G 1851T>C) GAG298ATG (1852G>A 1853A>T) GCC299GGA (1856C>G 1857C>A) TTC300TTT (1860C>T) CTT302TTG (1864C>T 1866T>G) AAT303ACT (1868A>C) CGA304CGC (1872A>C) CCT305CCC (1875T>C) CAG306GGT (1876C>G 1877A>G 1878G>T) GAT308GAC (1884T>C) CAC309TAC (1885C>T) CGT317AGC (1909C>A 1911T>C) CTC318TTG (1912C>T 1914C>G) CTG319AAA (1915C>A 1916T>A 1917G>A) GTC320ATC (1918G>A) TAC321TAT (1923C>T) CGG323CAG (1928G>A) ACT324GCT (1930A>G) CTA325CTG (1935A>G) AAA330CGG (1948A>C 1949A>G 1950A>G) GGG331GGC (1953G>C) GCA332GCC (1956A>C) GCA333TCA (1957G>T) AGG334AGA (1962G>A) CGC335CGG (1965C>G) ACC337ACT (1971C>T) GCC340GCT (1980C>T) GAA344GAG (1992A>G) GTC345GTG (1995C>G) TTG346ATG (1996T>A) CCA349CCG (2007A>G) ACA350AAC (2009C>A 2010A>C) CCC352CCT (2016C>T) CCG353CCC (2019G>C) TCC354TCG (2022C>G) GTT355GTA (2025T>A) CTA357CTT (2031A>T) GAA358GAG (2034A>G) CGT359AGG (2035C>A 2037T>G) CTA360CTC (2040A>C) GAG362GAA (2046G>A) GCT363GCC (2049T>C) TAT364TTC (2051A>T 2052T>C) AGA366CGG (2056A>C 2058A>G) TAT367TTC (2060A>T 2061T>C) CCA369CCT (2067A>T) CCC372CCT (2076C>T) TCT373ACC (2077T>A 2079T>C) TCT374TCA (2082T>A) GGA376GCC (2087G>C 2088A>C) CAA377CAG (2091A>G) AAG378AAA (2094G>A) GCG379GCC (2097G>C) GCG380TCA (2098G>T 2100G>A) ATG383CTG (2107A>C) TCC384GCC (2110T>G) TTT385TTC (2115T>C) ATC386ATT (2118C>T) TCT389TCG (2127T>G) GCC390GCT (2130C>T) CCG391CTG (2132C>T) ATT393ATC (2139T>C) AAA394AGG (2141A>G 2142A>G) TTA397CTT (2149T>C 2151A>T) CAA398CAG (2154A>G) AGG399AGA (2157G>A) GGA402GGG (2166A>G) CTC403TTA (2167C>T 2169C>A) GAC405GAG (2175C>G) CAT406GCT (2176C>G 2177A>C) TCC407GAG (2179T>G 2180C>A 2181C>G) TTG408TTA (2184G>A) CAG409CGT (2186A>G 2187G>T) CTC411CTA (2193C>A) ATA412GTG (2194A>G 2196A>G) AAG413AGA (2198A>G 2199G>A) GTA418GTG (2214A>G) CAT420TAC (2218C>T 2220T>C) AAG421AGA (2222A>G 2223G>A) AGA422AGG (2226A>G) GAG425GAA (2235G>A) GAA426GAG (2238A>G) GAA427GAG (2241A>G) CAA429GAA (2245C>G) GAA430CAG (2248G>C 2250A>G) GAG432AAA (2254G>A 2256G>A) AAA433GAA (2257A>G) ACA436AGA (2267C>G) GAG437GAA (2271G>A) AGA439AGG (2277A>G) AGA441GAA (2281A>G 2282G>A) CGG442AGA (2284C>A 2286G>A) GAC444GAT (2292C>T) AGG445AGA (2295G>A) CGC446CGG (2298C>G) CAG447CAA (2301G>A) AAA449AAG (2307A>G) AAC450AAT (2310C>T) ACC452ACT (2316C>T) AAA453AAG (2319A>G) GCG457GCA (2331G>A) GTA458GTG (2334A>G) GTA459GTT (2337A>T) AGT460GAA (2338A>G 2339G>A 2340T>A) GAG461GGG (2342A>G) AAA462AAG (2346A>G) GGG463AGC (2347G>A 2349G>C) TTC464AGC (2350T>A 2351T>G) AGA465AGG (2355A>G) GGG466GAG (2357G>A) CAG468GAG (2362C>G) GCA469AGA (2365G>A 2366C>G) GGG470GAT (2369G>A 2370G>T) AAT471TTT (2371A>T 2372A>T) CTG472AGG (2374C>A 2375T>G) AGC473AAA (2378G>A 2379C>A) AAC474ATT (2381A>T 2382C>T) GCA476TCA (2386G>T) ATG477_AGG478del (2389_2394delATGAGG) GCA479GGC (2396C>G 2397A>C) AGG481AGA (2403G>A) GAA482CAG (2404G>C 2406A>G) GGA483TCA (2407G>T 2408G>C) GGA483_AGA484insGGGAACCTGGGCAAT (2409_2410insGGGAACCTGGGCAAT) AGA484AGG (2412A>G) CCG485ACC (2413C>A 2415G>C) CCT486CCA (2418T>A) CTG487CTC (2421G>C) AAA489AAG (2427A>G) GAT490GAC (2430T>C) CAG491CAA (2433G>A) TGC492TGT (2436C>T) GCA493GCG (2439A>G) TAC494TAT (2442C>T) AGG498AAA (2453G>A 2454G>A) GGC499GGA (2457C>A) CAT500CAC (2460T>C) GAG504AAC (2470G>A 2472G>C) CGG507AAG (2479C>A 2480G>A) AAG509GGA (2485A>G 2486A>G 2487G>A) GCC511del (2491_2493delGCC) AGG512AAA (2495G>A 2496G>A) GAA513GGA (2498A>G) ACC514CCG (2500A>C 2502C>G) AAT515AAG (2505T>G) CTG517CTA (2511G>A) ACC518GCT (2512A>G 2514C>T) CTG519CTA (2517G>A) GGT520GAA (2519G>A 2520T>A) GGT520_GAC521insGAAGATAAA (2520_2521insGAAGATAAA) GAC521GAT (2523C>T)
pol protein (YP_009513211.1)	1	366	32.4%	1952	74.8%	366 (99.7%)	260 (70.8%)	1/0/0/0	0
Protein mutations:	M1L (2641A>T 2643G>A) M4L (2650A>C 2652G>A) G5K (2653G>A 2654G>A) S6E (2656T>G 2657C>A 2658C>A) R8K (2662C>A 2663G>A 2664G>A) T9S (2665A>T 2667A>C) V10W (2668G>T 2669T>G 2670C>G) A12M (2674G>A 2675C>T 2676T>G) S17Q (2689A>C 2690G>A 2691C>A) K18R (2692A>C 2693A>G 2694A>G) V19Q (2695G>C 2696T>A 2697T>G) K25R (2713A>C 2714A>G 2715G>A) L27T (2719C>A 2720T>C 2721T>C) L28V (2722T>G 2724G>T) K29D (2725A>G 2727A>C) I30L (2728A>T 2730T>G) Q32V (2734C>G 2735A>T 2736A>G) K33G (2737A>G 2738A>G 2739G>A) Q34R (2741A>G 2742A>G) A47V (2780C>T 2781T>A) L58M (2812C>A 2814A>G) K59G (2815A>G 2816A>G) Q63S (2827C>T 2828A>C 2829G>T) S65E (2833T>G 2834C>A 2835C>A) T66Q (2836A>C 2837C>A) E67G (2840A>G 2841G>A) G68R (2842G>A 2844C>A) Q70E (2848C>G 2850G>A) T72S (2854A>T 2856A>T) W73V (2857T>G 2858G>T) E74N (2860G>A 2862A>T) D75N (2863G>A) R76K (2866C>A 2867G>A 2868C>A) A78I (2872G>A 2873C>T) M79T (2876T>C 2877G>T) C80V (2878T>G 2879G>T 2880T>G) V82T (2884G>A 2885T>C) N84Q (2890A>C 2892C>A) E86D (2898G>T) E87D (2901G>T) H92Y (2914C>T 2916C>T) E93S (2917G>T 2918A>C 2919A>T) K94P (2920A>C 2921A>C 2922G>C) P95Q (2924C>A 2925G>A) P97K (2929C>A 2930C>A 2931T>G) S99D (2935T>G 2936C>A) I100Q (2938A>C 2939T>A 2940C>A) D101_P102insI (2943_2944insATA) P102Q (2945C>A) Q106E (2956C>G 2958A>G) L107Q (2960T>A 2961C>G) M110Q (2968A>C 2969T>A 2970G>A) V111A (2972T>C 2973T>C) K115T (2984A>C 2985G>C) N122K (3006T>G) V127Q (3019G>C 3020T>A) V129I (3025G>A 3027G>T) E130Q (3028G>C) S133A (3037T>G 3039A>C) D134S (3040G>A 3041A>G) S136T (3046T>A) A139S (3055G>T 3057T>A) M145L (3073A>T) K147R (3080A>G 3081G>A) R154W (3100A>T) I157V (3109A>G 3111C>T) F160L (3120C>A) L161I (3121T>A 3123G>C) D162Q (3124G>C 3126T>A) L163Q (3127T>C 3128T>A) C169V (3145T>G 3146G>T) K181R (3182A>G 3183A>G) S217A (3289T>G) S221E (3301A>G 3302G>A 3303C>A) H222R (3305A>G 3306C>G) T223N (3308C>A) S226T (3316T>A) K238R (3353A>G 3354G>A) N242T (3365A>C 3366C>T) E255G (3404A>G 3405A>T) K256T (3407A>C 3408A>G) N258R (3413A>G 3414T>A) L277I (3469C>A) S288N (3502T>A 3503C>A) A291I (3511G>A 3512C>T 3513T>C) L292Q (3515T>A 3516C>A) N293H (3517A>C) V297T (3529G>A 3530T>C 3531G>C) M298L (3532A>C 3534G>C) V307L (3559G>C 3561A>G) A309G (3566C>G 3567C>A) P310A (3568C>G 3570A>C) Y312K (3574T>A 3576C>A) R313Q (3578G>A 3579A>G) K316L (3586A>T 3587A>T) R320K (3598C>A 3599G>A 3600A>G) R321A (3601A>G 3602G>C 3603G>A) Q324L (3611A>T) K328D (3622A>G 3624G>C) V333A (3638T>C 3639G>C) L340I (3658C>A) E343R (3667G>A 3668A>G 3669G>A) L351S (3691T>A 3692T>G 3693G>T) K353R (3697A>C 3698A>G 3699A>G) K356Q (3706A>C) P361E (3721C>G 3722C>A 3723A>G)
Codon mutations:	ATG1TTA (2641A>T 2643G>A) AAG3AAA (2649G>A) ATG4CTA (2650A>C 2652G>A) GGA5AAA (2653G>A 2654G>A) TCC6GAA (2656T>G 2657C>A 2658C>A) CGG8AAA (2662C>A 2663G>A 2664G>A) ACA9TCC (2665A>T 2667A>C) GTC10TGG (2668G>T 2669T>G 2670C>G) GCT12ATG (2674G>A 2675C>T 2676T>G) GGG13GGT (2679G>T) GCG14GCC (2682G>C) ACG15ACA (2685G>A) GGC16GGG (2688C>G) AGC17CAA (2689A>C 2690G>A 2691C>A) AAA18CGG (2692A>C 2693A>G 2694A>G) GTT19CAG (2695G>C 2696T>A 2697T>G) TAC20TAT (2700C>T) CCT21CCA (2703T>A) ACC23ACT (2709C>T) AAG25CGA (2713A>C 2714A>G 2715G>A) CTT27ACC (2719C>A 2720T>C 2721T>C) TTG28GTT (2722T>G 2724G>T) AAA29GAC (2725A>G 2727A>C) ATT30TTG (2728A>T 2730T>G) CAA32GTG (2734C>G 2735A>T 2736A>G) AAG33GGA (2737A>G 2738A>G 2739G>A) CAA34CGG (2741A>G 2742A>G) GTG35GTA (2745G>A) TCA38TCG (2754A>G) TTC39TTT (2757C>T) TTG40CTG (2758T>C) ATA42ATC (2766A>C) CCC43CCT (2769C>T) GAA44GAG (2772A>G) CCT46CCA (2778T>A) GCT47GTA (2780C>T 2781T>A) CTG49CTT (2787G>T) TTA50CTA (2788T>C) GGC51GGT (2793C>T) AGG52AGA (2796G>A) CTC54TTA (2800C>T 2802C>A) CTC55CTG (2805C>G) CTA58ATG (2812C>A 2814A>G) AAA59GGA (2815A>G 2816A>G) ATC62ATT (2826C>T) CAG63TCT (2827C>T 2828A>C 2829G>T) TCC65GAA (2833T>G 2834C>A 2835C>A) ACA66CAA (2836A>C 2837C>A) GAG67GGA (2840A>G 2841G>A) GGC68AGA (2842G>A 2844C>A) CAG70GAA (2848C>G 2850G>A) GTA71GTG (2853A>G) ACA72TCT (2854A>T 2856A>T) TGG73GTG (2857T>G 2858G>T) GAA74AAT (2860G>A 2862A>T) GAC75AAC (2863G>A) CGC76AAA (2866C>A 2867G>A 2868C>A) GCC78ATC (2872G>A 2873C>T) ATG79ACT (2876T>C 2877G>T) TGT80GTG (2878T>G 2879G>T 2880T>G) TTA81TTG (2883A>G) GTC82ACC (2884G>A 2885T>C) CTG83CTC (2889G>C) AAC84CAA (2890A>C 2892C>A) TTG85TTA (2895G>A) GAG86GAT (2898G>T) GAG87GAT (2901G>T) TAC89TAT (2907C>T) TTA91CTA (2911T>C) CAC92TAT (2914C>T 2916C>T) GAA93TCT (2917G>T 2918A>C 2919A>T) AAG94CCC (2920A>C 2921A>C 2922G>C) CCG95CAA (2924C>A 2925G>A) GTC96GTA (2928C>A) CCT97AAG (2929C>A 2930C>A 2931T>G) TCT99GAT (2935T>G 2936C>A) ATC100CAA (2938A>C 2939T>A 2940C>A) GAC101GAT (2943C>T) GAC101_CCG102insATA (2943_2944insATA) CCG102CAG (2945C>A) TCA103TCC (2949A>C) CTC105TTG (2953C>T 2955C>G) CAA106GAG (2956C>G 2958A>G) CTC107CAG (2960T>A 2961C>G) ATG110CAA (2968A>C 2969T>A 2970G>A) GTT111GCC (2972T>C 2973T>C) GCC113GCA (2979C>A) GAG114GAA (2982G>A) AAG115ACC (2984A>C 2985G>C) GGT117GGG (2991T>G) GGA119GGT (2997A>T) CTG120TTG (2998C>T) GCC121GCA (3003C>A) AAT122AAG (3006T>G) GTC124GTT (3012C>T) CCA125CCC (3015A>C) GTG127CAG (3019G>C 3020T>A) GTA128GTT (3024A>T) GTG129ATT (3025G>A 3027G>T) GAA130CAA (3028G>C) TCA133GCC (3037T>G 3039A>C) GAT134AGT (3040G>A 3041A>G) GCC135GCT (3045C>T) TCA136ACA (3046T>A) GTG138GTA (3054G>A) GCT139TCA (3055G>T 3057T>A) GTT140GTC (3060T>C) CGA141AGA (3061C>A) CCA144CCC (3072A>C) ATG145TTG (3073A>T) AGC146AGT (3078C>T) AAG147AGA (3080A>G 3081G>A) GAA148GAG (3084A>G) GCC149GCT (3087C>T) CGG150CGA (3090G>A) GAG151GAA (3093G>A) GGT152GGA (3096T>A) ATC153ATT (3099C>T) AGG154TGG (3100A>T) CCC155CCG (3105C>G) CAC156CAT (3108C>T) ATC157GTT (3109A>G 3111C>T) TTC160TTA (3120C>A) TTG161ATC (3121T>A 3123G>C) GAT162CAA (3124G>C 3126T>A) TTG163CAG (3127T>C 3128T>A) GGG164GGC (3132G>C) ATT165ATC (3135T>C) CTG166CTA (3138G>A) GTA167GTT (3141A>T) TGC169GTC (3145T>G 3146G>T) CAG170CAA (3150G>A) TCG171TCC (3153G>C) CCC172CCT (3156C>T) AAC174AAT (3162C>T) ACC175ACT (3165C>T) CCT176CCC (3168T>C) TTG177CTG (3169T>C) TTA178CTA (3172T>C) CCT179CCG (3177T>G) GTA180GTT (3180A>T) AAA181AGG (3182A>G 3183A>G) AAA182AAG (3186A>G) GGA184GGG (3192A>G) GAC187GAT (3201C>T) CGG189CGA (3207G>A) GTC191GTA (3213C>A) CAA192CAG (3216A>G) GAT193GAC (3219T>C) AGG195AGA (3225G>A) AAC198AAT (3234C>T) AGA200AGG (3240A>G) GTA201GTG (3243A>G) ATT204ATA (3252T>A) CAT205CAC (3255T>C) CCC206CCA (3258C>A) ACA207ACG (3261A>G) CCC211CCT (3273C>T) CTA214CTC (3282A>C) CTC215TTG (3283C>T 3285C>G) AGT216AGC (3288T>C) TCC217GCC (3289T>G) CCC220CCT (3300C>T) AGC221GAA (3301A>G 3302G>A 3303C>A) CAC222CGG (3305A>G 3306C>G) ACC223AAC (3308C>A) TAT225TAC (3315T>C) TCA226ACA (3316T>A) GTT227GTA (3321T>A) TTA228TTG (3324A>G) CTC230TTA (3328C>T 3330C>A) GCT233GCC (3339T>C) TTT235TTC (3345T>C) CTC237CTG (3351C>G) AAG238AGA (3353A>G 3354G>A) CTA239TTA (3355C>T) AAC242ACT (3365A>C 3366C>T) CAG244CAA (3372G>A) TTG246CTT (3376T>C 3378G>T) TTC247TTT (3381C>T) GCG248GCC (3384G>C) TTT249TTC (3387T>C) GAA255GGT (3404A>G 3405A>T) AAA256ACG (3407A>C 3408A>G) GGC257GGA (3411C>A) AAT258AGA (3413A>G 3414T>A) ACT259ACC (3417T>C) GGC260GGG (3420C>G) CTA262CTC (3426A>C) ACT265ACC (3435T>C) CGG266CGA (3438G>A) CTA267CTG (3441A>G) CCG268CCC (3444G>C) GGA270GGG (3450A>G) TCT274TCC (3462T>C) CCC275CCG (3465C>G) CTC277ATC (3469C>A) TTC278TTT (3474C>T) GAT279GAC (3477T>C) GAG280GAA (3480G>A) CTC282CTA (3486C>A) CGG284AGG (3490C>A) GAT285GAC (3495T>C) GCA287GCC (3501A>C) TCC288AAC (3502T>A 3503C>A) GCT291ATC (3511G>A 3512C>T 3513T>C) CTC292CAA (3515T>A 3516C>A) AAC293CAC (3517A>C) CCC294CCT (3522C>T) GTA296GTG (3528A>G) GTG297ACC (3529G>A 3530T>C 3531G>C) ATG298CTC (3532A>C 3534G>C) CAA300CAG (3540A>G) TAT301TAC (3543T>C) GTT302GTG (3546T>G) CTC305CTG (3555C>G) CTG306CTT (3558G>T) GTA307CTG (3559G>C 3561A>G) GCC309GGA (3566C>G 3567C>A) CCA310GCC (3568C>G 3570A>C) ACG311ACC (3573G>C) TAC312AAA (3574T>A 3576C>A) CGA313CAG (3578G>A 3579A>G) AAA316TTA (3586A>T 3587A>T) GGG318GGT (3594G>T) ACA319ACG (3597A>G) CGA320AAG (3598C>A 3599G>A 3600A>G) AGG321GCA (3601A>G 3602G>C 3603G>A) CTC322CTA (3606C>A) TTA323CTG (3607T>C 3609A>G) CAG324CTG (3611A>T) CTA326TTG (3616C>T 3618A>G) AGT327TCT (3619A>T 3620G>C) AAG328GAC (3622A>G 3624G>C) TTG329CTA (3625T>C 3627G>A) GGA330GGC (3630A>C) CGA332AGA (3634C>A) GTG333GCC (3638T>C 3639G>C) TCG334TCT (3642G>T) GCC335GCT (3645C>T) AAA336AAG (3648A>G) CTT340ATT (3658C>A) CGG342AGG (3664C>A) GAG343AGA (3667G>A 3668A>G 3669G>A) GAA344GAG (3672A>G) GTT345GTA (3675T>A) ACG346ACA (3678G>A) TAT347TAC (3681T>C) CTC348TTG (3682C>T 3684C>G) TAT350TAC (3690T>C) TTG351AGT (3691T>A 3692T>G 3693G>T) CTA352TTG (3694C>T 3696A>G) AAA353CGG (3697A>C 3698A>G 3699A>G) GGG354GGC (3702G>C) AAG356CAG (3706A>C) AGA357CGA (3709A>C) ACC360ACG (3720C>G) CCA361GAG (3721C>G 3722C>A 3723A>G) GCC362GCA (3726C>A) CGA363CGG (3729A>G)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43