Genome Detective

NGS Details (SRR3458562_Metagenome_example): RD114 retrovirus

Assembly

Coverage Length

893 (6 contig(s))

Depth Of Coverage

2.1

Number Of Reads

Reads Per Million

1.03 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

RD114 retrovirus (Taxonomy ID: 11834)

Reference Genome

NC_009889.1

NT Identity (%)

93.0571

AA Identity (%)

90.625

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

1558.0 (NT) + 1416.0 (AA) = 2974.0

Concordance (%)

84.4407

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 1769 and ends at position 7988 relative to NC_009889.1 reference sequence.

NC_009889.1

SRR3458562_Metagenome_example-NC_009889.1-119-0

NC_009889.1

SRR3458562_Metagenome_example-NC_009889.1-119-0

TGAGAAGTCAGAACCCCCCACCTTTGCTACATAAATAACCGCTTTCATTTCGCTTCTGTAAAACCGCTTATGCGCCCCACCCTAACCGCTTTCATTTCGCTTCTGTAAAACCGCTTATGCGCCCCACCCTAGCCGGAAAGTCCCCAGCCGCTACGCAACCCGGGCCCCGAGTTGCATCAGCCGCTTCGCAACCCGGGCTCCGAGTTGCATCAGCCGAAAGAAACTTCATTTCCCAAGCTTCCCCGGGACGAAATTACCCACAACCCCAACCACCACCGAGCAGAGAGCCTATCGCCAGCCTGTATGCAAATGTAACTCAAAATGGTATAAAAGACCTGTAACCCCGTTTATCGGGGCTCTCCCGCTTTCTAACACTGGGGAGCCCTGGTGCACCAGTAAAGACTCTCTGCCGACGTCGGAGTGCCGCGTGGTTCTTTGCGCCAACTCTCATTCCATAGGGCCTAGGAGTTTGGCTCCTAACATTTGGTGCATTGGCCGGGAAACCGAGGGAAGGCAAGAGAACCCCGGCCCCGTCGGTGGATGACTCTCCGGCCCGGGCCACTGACGGACTGACTGAAGACAGACTTCTGTGCCTTTGTCTGCACACAGGTATTGTGTTCTATGTTTTGTCTCTGAACTGTGAATTCTGAGGCCGGCCGGCCACCTCCGTAGGAGTGTTGAAGGAGGACAGACGTGTCCTGAACCTTCACACCCCAGCCCCGAGGGACGCCTCGGTGGTGTTTGTAGGGGAGAACTGACAAGTTCGTCAGACTCCCCAAATCCGTAGGCAGGCCTCCCCTGCCATCTGAATCTGAATACTGGCCGCGGCTCCTTGGTTATTGTCTAGTCTGTGTTGTCTGGTCTGTGTCGACATTGTAGTCATCTTTGTGTATGTGTGTGTAAGTGTGCTGGTGTGGACGCGTGGACAGGACAGGACGACACAGCCATGGGACAGACATTGACTACTCCTCTAACTTTGACTCTGACTCATTTCTCGGAC

GTCCAAGCAAGAGCTCACAATCTTTCCCTTGAGGTTCGGAAAGGTCGATGGCGAACTTATTGTTCATCAGAGTGGCCCACCCTATCCGTAGGGTGGCCCCGGGATGGGACTTTTGACCTCTCTATTATATTACAGGTTAAGACGAAGGTAATGGATCCCGGACCACGAGGTCATCCAGATCAAATAGCCTATATCCTCACGTGGGAGGATCTCATTCGGAATCCTCCGGCATGGGTGAAACCCTTCCTCCCTTCCTGCCCCCTATCTCAGTCTACCCTTCTCCCCCTGAAAACCTCAAAAGACCGAGCCTCAACCCAACCTTCAGCCCCACCCAAACCGCCCAAACCAGTTCTTCCTGATGAGTCCCAAAAGGACCCTCCTCTCCTAGACGCTTTGTCCTCGCCGCCTCACAACCCCCTCCTACAGCCTCCACCCTATAATCCGCCCCTGGCCCCCGCCTTGACCCCGGTGGGCCCTACGTCCCCTCCTGCCTCCAGTTCCTCCTCCCTCTCCCCAACTTCTTCCCCCGCCTGTACGTCAGCCCCGTCCTCTACCCCAGCCCCACCCGATCTAACTCCCCAGACCCCACCTCAGACCCCCCGCCTCCGTCTCCGGCGATTGGATGACCCAAACGGCCCTCCCACTTGGCAATCTTCCCTGTTTCCTCTTCGGACAGTCAACCGGACTGTCCAATATTGGCCATTCTCTGCCTCCGATCTTTATAATTGGAAAACTCATAACCCTTCCTTTTCCCAAGAACCCCAGGCCCTAACCTCACTGATAGAATCCATCCTCCTCACACACCAGCCCACCTGGGACGACTGCCAGCAACTCCTACAGGTCCTTTTGACTACAGAGGAAAGGCAACGAGTTCTCCTGGAGGCCCGGAAAAATGTGCCAGGGCCTGGAGGCTTTCCAACCCAGCTCCCCAATGAAATAGATGAGGGGTTTCCCCTTACTCGCCCGGACTGGGACTATGAAACGGCTCCAGGTAGGGAGA

GTCTCCGAATCTATCGCCAGGCTCTGTTGGCGGGTCTCAAGGGGGCAGGAAAACGGCCCACCAATTTGGCCAAGGTAAGAACTATAATTCAAGGAAAAGAGGAAAGCCCCGCAGCCTTTATGGAACGGCTTCTAGAGGGGTTTCGGATGTATACTCCATTTACGCCCGAAGCTCCAGAACATAAGGCTACAGTGGCCATGTCGTTCATAGATCAGGCAGCATCCGATATAAAAGGAAAACTCCAAAGGTTAGATGGGATCCAAACCTATGGGTTGCAAGAACTAGTTAGGGAGGCAGAAAAGGTATATAACAAGAGGGAAACTCCAGAAGAAAAGGAGGCTAGGCTAGCAAAAGAGCAGGAAGCACGGGAGGAACGAAGAGATCGAAAGAGAGATAAACATCTAACTAAAATCCTGGCAGCTGTAGTGACAGAAAATAGAACAGGAAAGTCAGGGGAAACGAAGAGGCGGCCCAAAATAGAAAAAGACCAATGTGCCTATTGCAAAGAGCGCGGGCACTGGATCAAAGACTGCCCTAAGCGCCCTAGAGACTCAAAGAAATCTACCCCCGTACTCACCTTGGGCGAAGAGAGCGAGTAGGGACGTCAGGGCTCTGGAGCCCCCCCCGAGCCCCGGCTAACTTTATCTGTAGGGGGGCATCCCACCACCTTCCTGGTGGACACGGGAGCTCAACACTCGGTCTTAACCAAGGCAAATGGGCCCCTGTCCTCGCGTACCTCCTGGGTCCAAGGAGCGACAGGAAGGAAAATTCACAAATGGACTAACCGCCGCACGGTTGACCTAGGGCAAGGGACAGTGACACACTCCTTTCTGGTGGTACCCGAATGCCCGTACCCCCTTCTGGGACGAGACCTCCTGACCAAGCTTGGAGCCCAGATACACTTCTCCGAAACGGGGGCCCAAGTGCTAAACCGGGATGGCCAGCCTATCCAAGTCTTGACTGTGTCCTTACACGACGAACATAGACTTTTTGAAACCCC

GGTCACCACTAACCTCCTCGAAGCCTGGCTGCAGGACTTTCCCCAGGCCTGGGCAGAAACGGGAGGGCTCGGTCGAGCCAAATGTCAGGCCCCAATCATAATTGACCTAAAGCCCACGGCAATGCCTGTATCTATCAGACAGTATCCCATGAGCAAGGAGGCTCATATGGGCATTCAGCCACACATTACCAGGTTTCTAGAGCTTGGGGTCCTGCGACCTTGCCGCTCACCTTGGAATACCCCTCTCTTACCAGTGAAAAAACCTGGTACTCGGGACTACAGGCCCGTCCAAGACTTAAGGGAAGTCAACAAAAGGACTATGGATATCCATCCTACGGTCCCCAATCCCTATAACTTGCTCAGCACTCTGAGCCCAGACCGCACCTGGTACACAGTACTGGACCTAAAAGATGCATTCTTTTGCTTACCCTTGGCCCCCCAGAGCCAGGAACTGTTTGCTTTCGAATGGAGGGACCCTGAAAGAGGAATCTCAGGCCAATTAACCTGGACCCGCTTACCCCAGGGGTTCAAAAACTCCCCCACTCTCTTTGATGAGGCTCTCCACAGGGACCTAACTGACTTCCGGACTCAACACCCAGAAGTAACTCTACTCCAATATGTGGATGACCTTCTTCTGGCCGCCCCCACAGAGGAAGCCTGCACACGAGGTACCAAACATCTGCTTCGAGAATTGGGAGACAAAGGATACCGGGCATCCGCTAAGAAGGCCCAGATTTGCCAAACCAAAGTAACCTATCTGGGGTACATACTAAGTGAGGGGAAAAGATGGCTCACCCCTGGGCGAATAGAAACTGTGGCTCGCATTCCGCCGCCCCAGAGCCCCAGAGAGGTACGTGAATTCCTGGGAACTGCTGGGTTCTGTCGCTTATGGATACCTGGGTTCGCTGAGCTAGCCGCCCCCCTCTATGCCCTCACGAAAGAGAGTGCACCCTTCACCTGGCAGGAAAAACATCAGTCAGCCTTTGAGGCCCTAAAAGAG

GCCCTCCTTTCCGCCCCGGCTCTCGGGTTGCCAGACACCTCCAAGCCCTTTACCCTCTTCATAGACGAGAAACAAGGAATTGCCAAAGGAGTTCTAACCCAAAAACTAGGGCCCTGGAAGAGACCAGTAGCATACCTGTCCAAAAAGTTGGACCCTGTGGCAGCGGGGTGGCCCCCATGTCTTCGTATCATGGCAGCCACTGCTATGCTGGTCAAGGACTCTGCCAAATTAACCCTTGGACAGCCACTAACTGTTATCACCCCGCATGCTTTAGAGGCCATAGTGCGGCAACCACCAGACCGATGGATAACCAACGCACGCCTAACTCACTACCAGGCCCTCCTACTGGACACAGACCGCGTCCAATTTGGACCTCCGGTTACCTTGAACCCTGCCACGTTGCTACCGGCACCGAAAGACCAACAGAGCGCACACGATTGTCGGCAAGTACTGGCTGAGACCCATGGGACACGGGAAGATCTTAAAGATCAAGAGCTCCCAGATGCGGATCACTCTTGGTATACGGACGGGAGCAGTTACATCGACTCAGGTACCCGGAGGGCGGGAGCGGCGGTAGTAGATGGCCACCACATCATATGGGCACAATCACTACCTCCTGGCACGTCTGCCCAAAAGGCTGAGCTGATAGCACTCACCAAGGCCCTAGAGCTATCCGAAGGGAAAAAGGCTAACATATATACAGATAGCCGATATGCCTTTGCAACGGCTCATACACATGGGAGTATTTATGAAAGAAGGGGCCTACTAACCTCAGAAGGAAAAGAAATTAAAAATAAAGCTGAAATCATTGCATTATTAAAGGCCCTTTTTCTTCCCCGGAGAGTAGCCATAATTCATTGCCCCGGGCATCAGAAAGGACAAGACCCAATTGCAACAGGAAATAGACAGGCAGACCAAGTAGCCAGGCAAGTCGCTGTGGCAGAAACGTTGACTTTGACCAAGCTTGAAGAAACCAATCTTACGACCAACAAATATGCTT

ACACCCCAGAAGACCAGGAAGAGGCAAAGGCCATAGGGGCTATACTGAATCAGGACACTAAAGACTGGGAAAAAGAAGGAAAGATAGTCCTTCCCCGAAAGGAAGCCCTAGCAATGATCCAACAAATGCACGCCTGGACACATTTAAGTAATCGGAAGCTGAAGTCACTGATTGAAAAGACTGACTTCTTAATCCCTAAGGCAGGCACCCTCATAGAACAGGTGACCTCCGCCTGTAAGGTCTGTCAACAGGTAAACGCTGGGGCTACCCGAGTGCCAGAAGGAAAACGGACTCGTGGTAACCGCCCAGGAGTCTATTGGGAAATAGATTTTACTGAAGTAAAGCCTCACTATGCGGGGTATAAGTACCTATTAGTGTTTGTAGACACCTTTTCAGGATGGGTAGAAGCCTACCCCACCCGACAGGAAACGGCACACGTGGTAGCCAAGAAGATTTTAGAAGAAATCTTCCCCAGATTTGGACTTCCCAAGGTAATCGGGTCAGATAACGGGCCGGCCTTCGTTTCCCAGGTAAGTCAGGGGCTCGCCAGGACACTGGGGATTAATTGGAAATTACACTGTGCATATAGGCCCCAGAGCTCAGGACAGGTAGAAAGAATGAATAGAACAATAAAAGAGACCCTTACTAAATTGACCTTAGAGACTGGCTTAAAAGATTGGAGACGCCTCCTATCTCTGGCTTTGTTAAGAGCCAGAAATACGCCCAACCGTTTCGGGCTCACCCCATATGAAATCCTTTATGGGGGACCCCCCCCTTTGTCAACCTTGCTCAATTCCTTCTCCCCCTCCGATCCTAAGACTGATTTACAAGCCCGACTAAAAGGGCTGCAAGCGGTGCAGGCCCAAATCTGGACACCCCTGGCCGAATTGTACCGGCCAGGACATCCACAAACTAGCCACCCATTTCAGGTGGGAGACTCCGTGTACGTCCGGCGGCACCGCTCTCAAGGATTGGAGCCTCGTTGGAAGGGACCTTACAT

CGTCCTGCTGACCACGCCCACCGCCATAAAGGTTGACGGGATCGCCGCCTGGATTCACGCATCGCACGCCAAGGCAGCCCCAAAAACCCCTGGACCAGAAACTCCCAAAACCTGGAAGCTCCGCCGTTCGGAGAACCCTCTTAAGATAAGACTCTCCCGTGTCTGACTGCTAATCCACCTTGTCCCTGTACTAACCCAAAATGAAACTCCCAACAGGAATGGTCATTTTATGTAGCCTAATAATAGTTCGGGCAGGGTTTGACGACCCCCGCAAGGCTATCGCATTAGTACAAAAACAACATGGTAAACCATGCGAATGCAGCGGAGGGCAGGTATCCGAGGCCCCACCGAACTCCATCCAACAGGTAACTTGCCCAGGCAAGACGGCCTACTTAATGACCAACCAAAAATGGAAATGCAGAGTCACTCCAAAAAATCTCACCCCTAGCGGGGGAGAACTCCAGAACTGCCCCTGTAACACTTTCCAGGACTCGATGCACAGTTCTTGTTATACTGAATACCGGCAATGCAGGGCGAATAATAAGACATACTACACGGCCACCTTGCTTAAAATACGGTCTGGGAGCCTCAACGAGGTACAGATATTACAAAACCCCAATCAGCTCCTACAGTCCCCTTGTAGGGGCTCTATAAATCAGCCCGTTTGCTGGAGTGCCACAGCCCCCATCCATATCTCCGATGGTGGAGGACCCCTCGATACTAAGAGAGTGTGGACAGTCCAAAAAAGGCTAGAACAAATTCATAAGGCTATGCATCCTGAACTTCAATACCACCCCTTAGCCCTGCCCAAAGTCAGAGATGACCTTAGCCTTGATGCACGGACTTTTGATATCCTGAATACCACTTTTAGGTTACTCCAGATGTCCAATTTTAGCCTTGCCCAAGATTGTTGGCTCTGTTTAAAACTAGGTACCCCTACCCCTCTTGCGATACCCACTCCCTCTTTAACCTACTCCCTAGCAGACTCCCTAGCGAATGC

CTCCTGTCAGATTATACCTCCCCTCTTGGTTCAACCGATGCAGTTCTCCAACTCGTCCTGTTTATCTTCCCCTTTCATTAACGATACGGAACAAATAGACTTAGGTGCAGTCACCTTTACTAACTGCACCTCTGTAGCCAATGTCAGTAGTCCTTTATGTGCCCTAAACGGGTCAGTCTTCCTCTGTGGAAATAACATGGCATACACCTATTTACCCCAAAACTGGACAGGACTTTGCGTCCAAGCCTCCCTCCTCCCCGACATTGACATCATCCCGGGGGATGAGCCAGTCCCCATTCCTGCCATTGATCATTATATACATAGACCTAAACGAGCTGTACAGTTCATCCCTTTACTAGCTGGACTGGGAATCACCGCAGCATTCACCACCGGAGCTACAGGCCTAGGTGTCTCCGTCACCCAGTATACAAAATTATCCCATCAGTTAATATCTGATGTCCAAGTCTTATCCGGTACCATACAAGATTTACAAGACCAGGTAGACTCGTTAGCTGAAGTAGTTCTCCAAAATAGGAGGGGACTGGACCTACTAACGGCAGAACAAGGAGGAATTTGTTTAGCCTTACAAGAAAAATGCTGTTTTTATGCTAACAAGTCAGGAATTGTGAGAAACAAAATAAGAACCCTACAAGAAGAATTACAAAAACGCAGGGAAAGCCTGGCATCCAACCCTCTCTGGACCGGGCTGCAGGGCTTTCTTCCGTACCTCCTACCTCTCCTGGGACCCCTACTCACCCTCCTACTCATACTAACCATTGGGCCATGCGTTTTCAGTCGCCTCATGGCCTTCATTAATGATAGACTTAATGTTGTACATGCCATGGTGCTGGCCCAGCAATACCAAGCACTCAAAGCTGAGGAAGAAGCTCAGGATTGAGCTTCCGGGACAAAAGCAGGGGGGAATGAGAAGTCAGAACCCCCCACCTTTGCTACATAAATAACCGCTTTCATTTCGCTTCTGTAAAACCGCTTATGCGCC

CCACCCTAACCGCTTTCATTTCGCTTCTGTAAAACCGCTTATGCGCCCCACCCTAGCCGGAAAGTCCCCAGCCGCTACGCAACCCGGGCCCCGAGTTGCATCAGCCGCTTCGCAACCCGGGCTCCGAGTTGCATCAGCCGAAAGAAACTTCATTTCCCAAGCTTCCCCGGGACGAAATTACCCACAACCCCAACCACCACCGAGCAGAGAGCCTATCGCCAGCCTGTATGCAAATGTAACTCAAAATGGTATAAAAGACCTGTAACCCCGTTTATCGGGGCTCTCCCGCTTTCTAACACTGGGGAGCCCTGGTGCACCAGTAAAGACTCTCTGCCGACGTCGGAGTGCCGCGTGGTTCTTTGCGCCAACTCTCATTCCATAGGGCCTAGGAGTTTGGCTCCTAACA

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

................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTAACCTCACTAATAGAGTCTATCCTCCTCACACMCCAGCCTACCTGGGACGACTGCCAGCAGCYCTTACAGGTCCTTYTSACTACCGAGGMAAGGCAMCGAGTTCTCCTGGAGGCCCGGAAAAATGTGCCGGG..................................................................................................

....................................TCAAGGGGGCAGRGAAACGGCCCACCMATTTSGCCAAGGTAAGGACCATAAWCCAAGGAAAAGAGGAGAGCCCCGCAGCCTTTATGAAACGGCTTCTAGAGGGGTTTCGGATGTATACTCCATTTAACCCCGAGGC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CAGGATAACTCACCTGGACACGGCTACCTCAGGGATTCAAAAATTCACCCACCATCTTTGACGAGGCACTACACGAGGACCTGGGTGAGTACAGAAGGGAGCACCCAGAA...............................................................................................................................................................................................................................................................................................................................................................................................................

.....................................................................................................CTCCCAAAACCTGGAAGCTCCGCCGTTCGGAGAACCCTCTTAAGATAAGACTCTCCCGTGTCTGACTGCTAATCCACCTTGTCCCTGTACTAACCCAAAATGAAACTCCCAACAGGAATGGTCATTTTATGTAGCC...........CGGGCAGGGTTTGACGACCCCCGCAAGGCTATCGCATTAGTACAAAAACAACATGGTAAACCCTGTGAATGCAGCGGAGGGCAGGTATCTGAGGCCCCACCGAACTCCATCCAACAGGTAATTTGCCCAGGCAAGA........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCTACTCACCCTCCTACTCATACTAACCATTGGGCCCTGCGTTTTCAGTCGCCTCATGGCCTTCATTAATGATAGACTTAATGTTGTACATGCCATGGTGCTGGCCCAGCAATACCAAGCACTCAAAGCTGAGGAAGAAGCTCAGGATTGAGCTTCCGGGACAAAAGCAGGGGGGAATGAGAAGTCAGAACCCCCCACCTTTGCTACATAAATAACCGCTTTCATTTCGCTTCTGCAAAAC............

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gag

MGQTLTTPLTLTLTHFSDVQARAHNLSLEVRKGRWRTYCSSEWPTLSVGWPRDGTFDLSIILQVKTKVMDPGPRGHPDQIAYILTWEDLIRNPPAWVKPFLPSCPLSQSTLLPLKTSKDRASTQPSAPPKPPKPVLPDESQKDPPLLDALSSPPHNPLLQPPPYNPPLAPALTPVGPTSPPASSSSSLSPTSSPACTSAPSSTPAPPDLTPQTPPQTPRLRLRRLDDPNGPPTWQSSLFPLRTVNRTVQYWPFSASDLYNWKTHNPSFSQEPQALTSLIESILLTHQPTWDDCQQLLQVLLTTEERQRVLLEARKNVPGPGGFPTQLPNEIDEGFPLTRPDWDYETAPGRESLRIYRQALLAGLKGAGKRPTNLAKVRTIIQGKEESPAAFMERLLEGFRMYTPFTPEAPEHKATVAMSFIDQAASDIKGKLQRLDGIQTYGLQELVREAEKVYNKRETPEEKEARLAKEQEAREERRDRKRDKHLTKILAAVVTENRTGKSGETKRRPKIEKDQCAYCKERGHWIKDCPKRPRDSKKSTPVLTLGEESE*GRQGSGAPPEPRLTLSVGGHPTTFLVDTGAQHSVLTKANGPLSSRTSWVQGATGRKIHKWTNRRTVDLGQGTVTHSFLVVPECPYPLLGRDLLTKLGAQIHFSETGAQVLNRDGQPIQVLTVSLHDEHRLFETPVTTNLLEAWLQDFPQAWAETGGLGRAKCQAPIIIDLKPTAMPVSIRQYPMSKEAHMGIQPHITRFLELGVLRPCRSPWNTPLLPVKKPGTRDYRPVQDLREVNKRTMDIHPTVPNPYNLLSTLSPDRTWYTVLDLKDAFFCLPLAPQSQELFAFEWRDPERGISGQLTWTRLPQGFKNSPTLFDEALHRDLTDFRTQHPEVTLLQYVDDLLLAAPTEEACTRGTKHLLRELGDKGYRASAKKAQICQTKVTYLGYILSEGKRWLTPGRIETVARIPPPQSPREVREFLGTAGFCRLWIPGFAELAAPLYALTKES

..................................................................................................................................................................................................................................................................................LTSLIESILLTXQPTWDDCQQXLQVLXTTEXRXRVLLEARKNVPX............................................XKGAXKRPTXXAKVRTIXQGKEESPAAFMKRLLEGFRMYTPFNPEX.......................................................................................................................................................................................................................................................................................................................................................................................................................................................XG*LTWTRLPQGFKNSPTIFDEALHEDLGEYRREHPE...................................................................................................................

APFTWQEKHQSAFEALKEALLSAPALGLPDTSKPFTLFIDEKQGIAKGVLTQKLGPWKRPVAYLSKKLDPVAAGWPPCLRIMAATAMLVKDSAKLTLGQPLTVITPHALEAIVRQPPDRWITNARLTHYQALLLDTDRVQFGPPVTLNPATLLPAPKDQQSAHDCRQVLAETHGTREDLKDQELPDADHSWYTDGSSYIDSGTRRAGAAVVDGHHIIWAQSLPPGTSAQKAELIALTKALELSEGKKANIYTDSRYAFATAHTHGSIYERRGLLTSEGKEIKNKAEIIALLKALFLPRRVAIIHCPGHQKGQDPIATGNRQADQVARQVAVAETLTLTKLEETNLTTNKYAYTPEDQEEAKAIGAILNQDTKDWEKEGKIVLPRKEALAMIQQMHAWTHLSNRKLKSLIEKTDFLIPKAGTLIEQVTSACKVCQQVNAGATRVPEGKRTRGNRPGVYWEIDFTEVKPHYAGYKYLLVFVDTFSGWVEAYPTRQETAHVVAKKILEEIFPRFGLPKVIGSDNGPAFVSQVSQGLARTLGINWKLHCAYRPQSSGQVERMNRTIKETLTKLTLETGLKDWRRLLSLALLRARNTPNRFGLTPYEILYGGPPPLSTLLNSFSPSDPKTDLQARLKGLQAVQAQIWTPLAELYRPGHPQTSHPFQVGDSVYVRRHRSQGLEPRWKGPYIVLLTTPTAIKVDGIAAWIHASHAKAAPKTPGPETPKTWKLRRSENPLKIRLSRV*

RDV114RtrV_gp2

MKLPTGMVILCSLIIVRAGFDDPRKAIALVQKQHGKPCECSGGQVSEAPPNSIQQVTCPGKTAYLMTNQKWKCRVTPKNLTPSGGELQNCPCNTFQDSMHSSCYTEYRQCRANNKTYYTATLLKIRSGSLNEVQILQNPNQLLQSPCRGSINQPVCWSATAPIHISDGGGPLDTKRVWTVQKRLEQIHKAMHPELQYHPLALPKVRDDLSLDARTFDILNTTFRLLQMSNFSLAQDCWLCLKLGTPTPLAIPTPSLTYSLADSLANASCQIIPPLLVQPMQFSNSSCLSSPFINDTEQIDLGAVTFTNCTSVANVSSPLCALNGSVFLCGNNMAYTYLPQNWTGLCVQASLLPDIDIIPGDEPVPIPAIDHYIHRPKRAVQFIPLLAGLGITAAFTTGATGLGVSVTQYTKLSHQLISDVQVLSGTIQDLQDQVDSLAEVVLQNRRGLDLLTAEQGGICLALQEKCCFYANKSGIVRNKIRTLQEELQKRRESLASNPLWTGLQGFLPYLLPLLGPLLTLLLILTIGPCVFSRLMAFINDRLNVVHAMVLAQQYQALKAEEEAQD*

MKLPTGMVILCSX...RAGFDDPRKAIALVQKQHGKPCECSGGQVSEAPPNSIQQVICPGKX.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................XLLTLLLILTIGPCVFSRLMAFINDRLNVVHAMVLAQQYQALKAEEEAQD*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	1769	7988	10.6%	1558	87.2%	893 (100%)	831 (93.1%)	0/0
Mutations:	1780G>A 1786A>G 1789C>T 1803A>M 1810C>T 1831A>G 1833T>Y 1835C>T 1847T>Y 1849G>S 1855A>C 1860A>M 1867A>M 1900A>G 2049G>R 2050A>G 2063A>M 2068G>S 2080A>G 2083T>C 2088T>W 2089T>C 2104A>G 2123G>A 2163C>A 2164G>C 2170A>G 3496C>A 3497C>T 3500T>C 3502A>C 3511C>A 3514C>G 3515T>C 3520C>T 3526G>A 3535C>T 3538C>A 3544T>C 3545C>A 3553T>C 3559T>A 3562C>A 3566A>G 3567G>A 3574A>G 3575A>G 3576C>G 3580C>G 3582T>A 3584C>A 3586G>A 3588C>G 3589T>G 3590C>G 3592A>G 6311A>C 6314C>T 6338C>T 6370C>T 7784A>C 7983T>C
CDS

gag	275	1740	8.4%	685	66.8%	147 (100%)	126 (85.7%)	0/0/9/0	2
Protein mutations:	E393K (2123G>A) T406N (2163C>A 2164G>C) Q851* (3497C>T) L867I (3545C>A) R874E (3566A>G 3567G>A) T877G (3575A>G 3576C>G) D878E (3580C>G) F879Y (3582T>A) T881R (3588C>G 3589T>G) Q882E (3590C>G 3592A>G)
Codon mutations:	CTG278CTA (1780G>A) GAA280GAG (1786A>G) TCC281TCT (1789C>T) CAC286CMC (1803A>M) CCC288CCT (1810C>T) CAA295CAG (1831A>G) CTC296CYC (1833T>Y) CTA297TTA (1835C>T) TTG301YTS (1847T>Y 1849G>S) ACA303ACC (1855A>C) GAA305GMA (1860A>M) CAA307CAM (1867A>M) CCA318CCG (1900A>G) GGA368GRG (2049G>R 2050A>G) AAT373MAT (2063A>M) TTG374TTS (2068G>S) AGA378AGG (2080A>G) ACT379ACC (2083T>C) ATT381AWC (2088T>W 2089T>C) GAA386GAG (2104A>G) GAA393AAA (2123G>A) ACG406AAC (2163C>A 2164G>C) GAA408GAG (2170A>G) GGC850GGA (3496C>A) CAA851TAA (3497C>T) TTA852CTC (3500T>C 3502A>C) ACC855ACA (3511C>A) CGC856CGG (3514C>G) TTA857CTA (3515T>C) CCC858CCT (3520C>T) GGG860GGA (3526G>A) AAC863AAT (3535C>T) TCC864TCA (3538C>A) ACT866ACC (3544T>C) CTC867ATC (3545C>A) GAT869GAC (3553T>C) GCT871GCA (3559T>A) CTC872CTA (3562C>A) AGG874GAG (3566A>G 3567G>A) CTA876CTG (3574A>G) ACT877GGT (3575A>G 3576C>G) GAC878GAG (3580C>G) TTC879TAC (3582T>A) CGG880AGA (3584C>A 3586G>A) ACT881AGG (3588C>G 3589T>G) CAA882GAG (3590C>G 3592A>G)
RDV114RtrV_gp2	1	566	19.3%	731	96.7%	109 (100%)	106 (97.2%)	0/0/0/0	1
Protein mutations:	T57I (6370C>T)
Codon mutations:	CCA37CCC (6311A>C) TGC38TGT (6314C>T) TCC46TCT (6338C>T) ACT57ATT (6370C>T) CCA528CCC (7784A>C)
Proteins

gag-pol precursor polyprotein (YP_001497148.1)	275	1740	8.4%	685	66.8%	147 (100%)	126 (85.7%)	0/0/9/0	2
Protein mutations:	E393K (2123G>A) T406N (2163C>A 2164G>C) Q851* (3497C>T) L867I (3545C>A) R874E (3566A>G 3567G>A) T877G (3575A>G 3576C>G) D878E (3580C>G) F879Y (3582T>A) T881R (3588C>G 3589T>G) Q882E (3590C>G 3592A>G)
Codon mutations:	CTG278CTA (1780G>A) GAA280GAG (1786A>G) TCC281TCT (1789C>T) CAC286CMC (1803A>M) CCC288CCT (1810C>T) CAA295CAG (1831A>G) CTC296CYC (1833T>Y) CTA297TTA (1835C>T) TTG301YTS (1847T>Y 1849G>S) ACA303ACC (1855A>C) GAA305GMA (1860A>M) CAA307CAM (1867A>M) CCA318CCG (1900A>G) GGA368GRG (2049G>R 2050A>G) AAT373MAT (2063A>M) TTG374TTS (2068G>S) AGA378AGG (2080A>G) ACT379ACC (2083T>C) ATT381AWC (2088T>W 2089T>C) GAA386GAG (2104A>G) GAA393AAA (2123G>A) ACG406AAC (2163C>A 2164G>C) GAA408GAG (2170A>G) GGC850GGA (3496C>A) CAA851TAA (3497C>T) TTA852CTC (3500T>C 3502A>C) ACC855ACA (3511C>A) CGC856CGG (3514C>G) TTA857CTA (3515T>C) CCC858CCT (3520C>T) GGG860GGA (3526G>A) AAC863AAT (3535C>T) TCC864TCA (3538C>A) ACT866ACC (3544T>C) CTC867ATC (3545C>A) GAT869GAC (3553T>C) GCT871GCA (3559T>A) CTC872CTA (3562C>A) AGG874GAG (3566A>G 3567G>A) CTA876CTG (3574A>G) ACT877GGT (3575A>G 3576C>G) GAC878GAG (3580C>G) TTC879TAC (3582T>A) CGG880AGA (3584C>A 3586G>A) ACT881AGG (3588C>G 3589T>G) CAA882GAG (3590C>G 3592A>G)
envelope glycoprotein (YP_001497149.1)	1	566	19.3%	731	96.7%	109 (100%)	106 (97.2%)	0/0/0/0	1
Protein mutations:	T57I (6370C>T)
Codon mutations:	CCA37CCC (6311A>C) TGC38TGT (6314C>T) TCC46TCT (6338C>T) ACT57ATT (6370C>T) CCA528CCC (7784A>C)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43