Genome Detective

NGS Details (SRR3458562_Metagenome_example): Mouse mammary tumor virus

Assembly

Coverage Length

587 (3 contig(s))

Depth Of Coverage

2.4

Number Of Reads

Reads Per Million

0.71 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

Mouse mammary tumor virus (Taxonomy ID: 11757)

Reference Genome

NC_001503.1

NT Identity (%)

63.5593

AA Identity (%)

54.6419

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

296.0 (NT) + 1628.0 (AA) = 1924.0

Concordance (%)

50.1303

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 1672 and ends at position 3412 relative to NC_001503.1 reference sequence.

NC_001503.1

SRR3458562_Metagenome_example-NC_001503.1-62-0

NC_001503.1

SRR3458562_Metagenome_example-NC_001503.1-62-0

NC_001503.1

SRR3458562_Metagenome_example-NC_001503.1-62-0

GCAACAGTCCTAACATTCACCTCTCGTGTGTTTGTGTCTGTTCGCCATCCCGTCTCCGCTCGTCACTTATCCTTCACTTTCCAGAGGGTCCCCCCGCAGACCCCGGTGACCCTCAGGTCGGCCGACTGCGGCAGCTGGCGCCCGAACAGGGACCCTCGGATAAGTGACCCTTGTCTCTATTTCTACTATTTTGTGTTCGTCTTGTTTTGTCTCTATCTTATCTGGCTATTATCACAAGAGCGGAACGGACTCACCACAGGGAACTGCAGTCTCGCCTACAGAGAAGAGGTAGGTTACGGTGAGCCATTGGAAATGGGGGTCTCGGGATCAAAAGGGCAGAAACTCTTTGTTTCTGTTCTACAAAGACTCCTCTCAGAGAGGGGTCTTCATGTGAAAGAGAGCAGTGCAATAGAGTTTTATCAGTTCCTAATAAAGGTCTCTCCTTGGTTTCCCGAAGAAGGAGGATTAAATTTACAAGATTGGAAAAGGGTGGGAAGAGAGATGAAGAGGTACGCAGCAGAACATGGGACGGATAGTATACCAAAGCAGGCTTACCCCATTTGGCTTCAGTTGAGAGAGATACTGACAGAGCAATCAGACTTGGTTTTGTTATCTGCAGAAGCCAAGTCCGTGACTGAAGAGGAATTAGAGGAAGGTTTAACCGGACTACTATCGACAAGTTCACAGGAAAAAACTTATGGGACTAGGGGAACAGCATATGCAGAAATAGATACAGAGGTAGACAAGCTGTCTGAACATATTTATGATGAACCATATGAAGAAAAGGAGAAGGCAGATAAAAATGAGGAAAAGGACCATGTTAGAAAAATAAAGAAGGTAGTACAAAGAAAAGAAAATAGTGAGGGTAAGAGAAAAGAGAAGGATTCAAAGGCCTTTTTAGCCACAGATTGGAACGATGATGACCTGTCCCCTGAGGATTGGGACGATTTAGAGGAACAAGCGGCACATTATCATGATGATGATGAGCTAATCCTTCCAG

TAAAAAGGAAGGTGGTTAAGAAGAAACCTCAGGCACTCAGAAGGAAACCCCTGCCTCCGGTGGGTTTTGCAGGAGCGATGGCAGAGGCCAGGGAAAAAGGAGATTTGACTTTTACGTTTCCTGTAGTTTTTATGGGAGAGAGTGATGAAGATGACACGCCTGTTTGGGAACCGCTGCCATTGAAAACCTTAAAGGAATTGCAATCGGCAGTTAGGACCATGGGACCATCTGCTCCCTACACCCTGCAGGTGGTAGACATGGTGGCTAGTCAATGGCTCACCCCGAGTGACTGGCACCAAACAGCCAGAGCTACCTTGTCTCCTGGAGACTATGTTTTATGGAGAACTGAATATGAAGAGAAAAGTAAAGAAATGGTACAAAAGGCTGCAGGCAAGCGAAAGGGCAAGGTCTCTCTTGATATGTTACTGGGGACTGGCCAATTCCTGTCCCCTTCTTCTCAGATAAAATTGTCTAAGGATGTCTTAAAAGATGTCACCACAAATGCTGTGTTAGCATGGAGGGCCATTCCGCCTCCTGGAGTTAAAAAGACTGTATTAGCAGGATTAAAACAGGGAAATGAAGAGTCTTATGAGACTTTCATTTCAAGGCTCGAGGAAGCTGTTTACCGAATGATGCCCAGAGGGGAAGGGTCGGATATATTGATCAAACAATTGGCGTGGGAGAATGCAAATTCATTGTGTCAGGATCTCATCCGCCCAATACGTAAAACAGGAACTATACAGGATTATATTCGTGCTTGTCTGGACGCTTCTCCCGCAGTTGTTCAGGGTATGGCATATGCAGCAGCCATGAGAGGACAAAAGTATTCTACCTTTGTAAAGCAAACATATGGTGGG---GGAAAAGGAGGTCAAGGAGCAGAAGGGCCA---GTTTGTTTTTCCTGTGGTAAGACAGGACACATCAGAAAAGACTGTAAGGATGAAAAGGGCTCAAAAAGGGCCCCTCCTGGGCTCTGCCCCAGATGTAAGAAAGGCTA

TCACTGGAAGAGTGAGTGTAAATCTAAATTTGACAAAGATGGGAATCCACTTCCTCCCTTGGAAACTAATGCTGAAAATTCAAAAAACTTGTAAAGGGGCAGTCCCCTAGCCCCGCTCAAAAGGGGGATGGAGTTAAGGGCTCAGGATTAAATCCTGAAGCCCCACCTTTCACAATACATGATTTGCCTCGAGGCACCCCTGGAAGTGCAGGTTTAGACCTGTCATCACAGAAGGATTTGATCCTCTCTCTAGAAGATGGAGTATCATTGGTACCCACCTTAGTGAAAGGCACCCTCCCTGAAGGGACTACTGGACTAATAATAGGTAGAAGTTCTAATTATAAAAAGGGACTTGAGGTTTTACCAGGAGTCATTGACTCCGATTTCCAAGGAGAAATCAAGGTTATGGTTAAGGCCGCAAAAAATGCGGTCATCATTCACAAAGGAGAAAGAATAGCACAACTGCTGTTGCTGCCATATTTAAAATTACCCAATCCTGTAATCAAGGAAGAACGAGGCTCAGAAGGCTTCGGATCAACAAGTCATGTGCATTGGGTGCAGGAAATAAGTGACTCCAGACCCATGCTTCACATTTACTTAAATGGAAGAAGATTCCTCGGTCTCTTGGATACCGGGGCAGATAAAACTTGCATAGCAGGCAGAGACTGGCCAGCTAATTGGCCCATTCACCAAACTGAGAGTTCTCTTCAAGGTTTAGGCATGGCCTGTGGGGTGGCGCGTAGTAGTCAGCCACTCCGTTGGCAACATGAGGATAAATCAGGAATTATACATCCTTTTGTGATCCCTACACTGCCTTTCACCTTATGGGGAAGAGATATTATGAAAGATATAAAGGTCAGATTGATGACAGACTCACCAGATGATTCACAGGATTTATGATAGGGGCCATTGAGAGCAATCTCTTTGCAGACCAAATATCTTGGAAGTCAGACCAGCCTGTATGGCTTAATCAATGGCCCCTTAAACAAGAAAAGTTACA

GGCTTTACAACAGTTAGTGACAGAACAATTACAACTGGGCCACTTAGAAGAGAGCAATAGCCCTTGGAATACGCCTGTTTTTGTCATTAAAAAGAAGTCAGGAAAATGGAGACTGTTACAAGACCTACGTGCAGTTAATGCTACAATGCACGATATGGGAGCATTACAACCCGGCTTGCCGTCCCCTGTAGCAGTCCCTAAAGGATGGGAAATAATCATAATAGATCTACAAGATTGCTTTTTTAATATAAAACTGCATCCTGAAGATTGTAAAAGATTTGCTTTTAGTGTGCCCTCCCCTAATTTTAAGAGACCTTATCAAAGATTCCAATGGAAAGTTTTGCCCCAGGGTATGAAAAATAGCCCTACTTTATGTCAAAAATTTGTGGACAAAGCTATATTGACTGTAAGGGATAAATACCAAGACTCATATATTGTGCATTACATGGATGACATTCTTTTGGCACACCCATCAAGATCCATTGTCGATGAAATACTTACTTCCATGATACAGGCCCTTAACAAACATGGCCTTGTAGTATCCACAGAGAAGATTCAAAAATATGATAATCTCAAATATTTGGGAACTCATATACAGGGTGATTCAGTGTCTTATCAAAAATTACAGATTAGGACAGATAAATTAAGAACCTTAAATGATTTCCAAAAGCTATTAGGAAATATTAATTGGATACGTCCTTTCTTAAAATTAACTACGGGAGAGTTAAAACCTCTCTTTGAAATTCTTAATGGAGATTCTAATCCGATCTCAACAAGAAAACTTACTCCTGAGGCATGCAAAGCTCTTCAATTAATGAATGAGAGACTATCTACCGCTCGGGTAAAGAGGCTAGATTTATCACAGCCTTGGTCTCTATGTATATTAAAGACTGAATATACCCCCACAGCATGCCTCTGGCAGGATGGAGTTGTAGAATGGATACATTTGCCTCATATTTCACCAAAGGTGATTACTCCTTATGATATCTTTTGTACACAA

CTTATTATTAAGGGCCGACACCGCTCTAAAGAATTATTTAGTAAAGACCCTGATTATATTGTTGTGCCCTACACCAAAGTTCAATTTGATCTCCTATTACAAGAAAAGGAAGATTGGCCTATTTCTTTATTAGGGTTCTTGGGAGAGGTTCATTTCCATCTTCCAAAAGACCCTTTGCTTACATTTACCCTACAAACTGCCATTATTTTTCCTCACATGACCTCTACCACACCACTAGAGAAAGGAATTGTGATTTTTACAGACGGGTCAGCAAATGGCCGTTCGGTAACATATATACAAGGAAGGGAGCCTATAATTAAAGAAAATACACAAAACACAGCCCAACAGGCTGAAATTGTGGCAGTCATTACAGCCTTTGAGGAAGTGAGTCAACCCTTTAATTTGTATACTGATTCTAAATATGTGACAGGGTTGTTTCCCGAAATCGAAACTGCAACTTTGTCACCCAGAACAAAAATTTACACAGAACTGAAACATTTACAAAGGTTAATCCACAAGAGACAAGAAAAATTTTACATTGGTCATATCAGAGGACACACTGGACTTCCCGGTCCTTTGGCACAGGGAAATGCCTATGCAGATTCTTTAACAAGAATTCTGACCGCTTTAGAGTCAGCTCAAGAAAGCCACGCACTACATCATCAAAATGCCGCGGCGCTTAGGTTTCAGTTTCACATCACTCGTGAACAAGCGCGAGAAATAGTAAAATTATGTCCCAATTGCCCCGACTGGGGGCACGCGCCGCAATTAGGGGTAAACCCCAGGGGCCTTAAGCCCCGAGTTCTATGGCAAATGGATGTTACTCATGTTTCAGAATTTGGAAAATTAAAATATGTACATGTGACAGTGGATACTTATTCTCATTTTACTTTCGCTACCGCCCGAACGGGCGAAGCAACCAAGGATGTGTTACAACACTTGGCTCAAAGCTTTGCATACATGGGCATTCCTCAAAAAATAAAAACAGATAATGCCCCTG

CATATGTGTCTCGTTCAATACAAGAATTTCTGGCCAGATGGAAAATATCTCACGTCACGGGGATCCCCTACAATCCCCAAGGACAGGCCATTGTTGAACGAACGCACCAAAATATAAAGGCACAGCTTAATAAACTTCAAAAGGCTGGAAAATACTATACACCCCATCATCTGTTGGCACACGCTCTTTTTGTGCTGAATCATGTAAATATGGACAATCAAGGCCATACAGCGGCCGAAAGACATTGGGGTCCAATCTCAGCCGATCCAAAACCTATGGTCATGTGGAAAGACCTTCTCACAGGGTCCTGGAAAGGACCCGATGTCCTAATAACAGCCGGACGAGGCTATGCTTGTGTTTTTCCACAGGATGCCGAAACACCAATCTGGGTCCCCGACCGATTCATCCGACCTTTTACTGAGCGGAAAGAAGCAACGCCCACACCTGGCACTGCGGAGAAAACGCCGCCGCGAGATGAGAAAGATCAACAGGAAAGTCCCAAGAATGAATCTAGTCCCCATCAAAGAGAAGACGGCTTGGCAACATCTGCAGGCGTTGATCTCCGAAGCGGAGGAGGTCCTTAAAACCTCACAAACTCCCCAAACCTCTTTGACCTTATTTCTTGCTTTGTTGTCTGTCCTCGGCCCCCCGCCTGTGACAGGGGAGAGTTATTGGGCCTACCTACCTAAACCACCTATTCTCCATCCCGTGGGATGGGGAAGTACAGACCCCATTAGAGTTCTGACAAATCAAACCATGTATTTGGGTGGTTCGCCTGACTTTCATGGGTTCAGAAATATGTCTGGTAATGTACATTTTGAGGGGAAGTCTGATACGCTCCCCATTTGCCTTTCCTTCTCCTTTTCTACCCCCACGGGCTGCTTTCAAGTAGACAAGCAAGTATTTCTTTCTGATACACCCACGGTTGATAATAATAAACCTGGGGGAAAGGGTGATAAAAGGCGTATGTGGGAACTTTGGTTGACTACCTTGGGGAACT

CAGGGGCCAATACAAAACTGGTCCCTATAAAAAAGAAGTTGCCCCCCAAATATCCTCACTGCCAGATCGCCTTTAAGAAGGACGCCTTCTGGGAGGGAGACGAGTCTGCTCCTCCACGGTGGTTGCCTTGCGCCTTCCCTGACCAGGGGGTGAGTTTTTCTCCAAAAGGGGCCCTTGGGTTACTTTGGGATTTCTCCCTTCCCTCGCCTAGTGTAGATCAGTCAGATCAGATTAAAAGCAAAAAGAATCTATTTGGAAATTATACTCCCCCTGTCAATAAAGAGGTTCATCGATGGTATGAAGCAGGATGGGTAGAACCTACTTGGTTCTGGGAAAATTCTCCTAAGGATCCCAATGATAGAGATTTCACTGCACTAGTCCCCCATACAGAATTGTTTCGCTTAGTCGCAGCCTCAAGACATCTTATTCTCAAAAGGCCAGGATTTCAAGAACATGAGATGATTCCTACATCTGCCTGTGTTACTTACCCTTATGCCATATTATTAGGATTACCTCAGTTAATAGATATAGAGAAAAGAGGATCTACTTTTCATATTTCCTGTTCTTCTTGTAGATTGACTAATTGTTTAGACTCTTCTGCCTACGACTATGCAGCGATCATAGTCAAGAGGCCGCCATATGTGCTGCTACCTGTAGATATTGGTGATGAACCATGGTTTGATGATTCTGCCATTCAAACCTTTAGGTATGCCACAGATTTAATTCGAGCTAAGCGATTCGTCGCAGCCATTATCCTGGGCATATCTGCTTTGATTGCTATTATTACTTCCTTTGCTGTAGCTACTACTGCCTTAGTTAAGGAGATGCAAACTGCTACGTTTGTTAATAATCTTCATAGGAATGTTACATTAGCCTTATCTGAACAACGGATAATAGATTTAAAATTAGAAGCTAGACTTAATGCTTTAGAAGAAGTAGTTTTAGAGTTGGGACAAGATGTGGCCAATTTAAAGACCAGAATGTCCACTAGGTGTCATGC

AAATTATGACTTTATCTGCGTTACACCTTTACCCTATAATGCTACTGAGAACTGGGAAAGAACCAGGGCTCATTTATTGGGCATTTGGAATGATAATGAGATTTCATATAACATACAGGAGTTAACCAACCTGATTAGTGATATGAGCAAACAACATATTGATGCAGTGGACCTTAGTGGCTTGGCTCAGTCTTTTGCCAATGGAGTGAAGGCTTTAAATCCATTAGATTGGACACAATATTTCATTTTTATAGGTGTTGGAGCCCTGCTTTTAGTCATTGTACTTATGATTTTCCCCATTGTTTTCCAGTGCCTTGCGAAGAGCCTTGACCAAGTGCAGTCAGATCTTAACGTGCTTCTTTTAAAAAAGAAAAAAGGGGGAAATGCCGCGCCTGCAGCAGAAATGGTTGAACTCCCGAGAGTGTCCTACACTTAGGGGAGAAGCAGCCAAGGGGTTGTTTCCCACCAAGGACGACCCGTCTGCGCACAAACGGATGAGCCCATCAGACAAAGACATACTCATTCTCTGCTGCAAACTTGGCATAGCTCTGCTTTGCCTGGGGCTATTGGGGGAAGTTGCGGTTCGTGCTCGCAGGGCTCTCACCCTTGACTCTTTTAATAGCTCTTCTGTGCAAGATTACAATCTAAACGATTCGGAGAACTCGACCTTCCTCCTGAGGCAAGGACCACAGCCAACTTCCTCTTACAAGCCGCATCAACCTTGTCCTTCAGAAATAGAAATAAGAATGCTTGCTAAAAATTATATTTTTACCAATAAGACCAATCCAATAGGTAGATTATTAGTTACTATGTTAAGAAATGAATCATTACCTTTTAGTACTATTTTTACTCAAATTCAAAGGTTAGAAATGGGAATAGAAAATAGAAAGAGACACTCAACCTCAGTTGAAGAACAGGTGCAGGGACTAAGGGCCTCAGGCCTAGAAGTAAAAAGGGGAAAGAGGAGTGCGCTTGTCAAAATAGGAGACAGGTGGTGGCA

ACCAGGGACTTATAGGGGACCTTACATCTACAGACCAACAGATGCCCCCTTACCGTATACAGGAAGATATGACCTAAATTTTGATAGGTGGGTCACAGTCAATGGCTATAAAGTGTTATACAGGTCCCTCTCCTTTCGTGAAAGGCTCGCCAGGGCTAGACCTCCTTGGTGTATGTTGACTCAGGAAGAGAAAAACGACATGAAACAACAGGTACATGATTATATTTATTTGGGAACAGGAATGAGCAGCATTTGGGGAAAGATTTTTCATACCAAGGAGAGGACAGTGGCTGCACTAATAGAGCACTATTCTGCAAAGACTTATGGCATGAGTTATTATGATTAGCCTTTATTAGCCCAATCTTGTGGTTCCCAAGGTTTAAGTAAGTTCATGGTCACAGACTGTTCTTAAAACAAGGATGTGAGACAAGTGGTTTCCTGACTTGGCTTGGTATCAAATGTTTTGATCTAAGCTCTAAATGCTCTAACCTCCTATGTTCTTTTGGATTCTATCCAAGTTTTATGTAAATGCTTATGTAAACCATGATATAAAAGAGTGCTAAATTTTTGAGTAAACTTGCAACAGTCCTAACATTCACCTCTCGTGTGTTTGTGTCTGTTCGCCATCCCGTCTCCGCTCGTCACTTATCCTTCACTTTCCAGAGGGTCCCCCCGCAGACCCCGGTGACCCTCAGGTCGGCCGACTGCGGCACGTCAGCTCGAGCAGAACCACCCGTGAGTTAGGTCGAGCAGAGCCAAAGCCCCCGGTGCTTCGTCGCGGGTTCGCTCGCTAGCTATCTGGATCACTCCC

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

...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TTAGCCTTTGAGAATGCTAATGCTCCTTGCCAAACACTGTTGCGACCAATTCGAAAGTTTGGGTCACTAACAGACTACATTAAACAATGTGCTGACTTTACGCCAGCCTTCATGCAAGGAGTTGCCATGGCAGCCGCCTTAAAAGGGGAAAGC---CCTCTTTATTGTATGCAAACTATGACTAAGAAAGGAAATAGAGCTGTGAGAGTAGATGGTGAAAATGCCTGCTTTTCTTGTGGACAACAGGGACACTTTAGTAGACAATGCCCCG..........................................................

.......................................................AATAGTCCTTGGAACTCTCCCATTCTCATTATCAAAAAGAAATCTGGAAAATGGAGATTGTTACAAGATCTGAGAGCCATTAGTGAGACCATGCAAGATATGGGGGTCCTACAACCCGGCTT.........................................TTATAGATTTGCAAGACTGTTTTTTCAACATCCCCTTAGACCCTAAGGACAGGCCCCGATTTGCCTTTAGCTTACCTTCAGAAAACTTGAGGAGACCTTATCAGAGATTTCAGTGGAAAGTGCTGCCGCAAGGAATGAAAAACAGCCCAACGTTGTGCCAAAAATTTGTTGATATGGCCTTAATGCAGGTCAGGCAAAAA......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

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gag

MGVSGSKGQKLFVSVLQRLLSERGLHVKESSAIEFYQFLIKVSPWFPEEGGLNLQDWKRVGREMKRYAAEHGTDSIPKQAYPIWLQLREILTEQSDLVLLSAEAKSVTEEELEEGLTGLLSTSSQEKTYGTRGTAYAEIDTEVDKLSEHIYDEPYEEKEKADKNEEKDHVRKIKKVVQRKENSEGKRKEKDSKAFLATDWNDDDLSPEDWDDLEEQAAHYHDDDELILPVKRKVVKKKPQALRRKPLPPVGFAGAMAEAREKGDLTFTFPVVFMGESDEDDTPVWEPLPLKTLKELQSAVRTMGPSAPYTLQVVDMVASQWLTPSDWHQTARATLSPGDYVLWRTEYEEKSKEMVQKAAGKRKGKVSLDMLLGTGQFLSPSSQIKLSKDVLKDVTTNAVLAWRAIPPPGVKKTVLAGLKQGNEESYETFISRLEEAVYRMMPRGEGSDILIKQLAWENANSLCQDLIRPIRKTGTIQDYIRACLDASPAVVQGMAYAAAMRGQKYSTFVKQTYGG-GKGGQGAEGP-VCFSCGKTGHIRKDCKDEKGSKRAPPGLCPRCKKGYHWKSECKSKFDKDGNPLPPLETNAENSKN

gag-pro

LVKGQSPSPAQKGDGVKGSGLNPEAPPFTIHDLPRGTPGSAGLDLSSQKDLILSLEDGVSLVPTLVKGTLPEGTTGLIIGRSSNYKKGLEVLPGVIDSDFQGEIKVMVKAAKNAVIIHKGERIAQLLLLPYLKLPNPVIKEERGSEGFGSTSHVHWVQEISDSRPMLHIYLNGRRFLGLLDTGADKTCIAGRDWPANWPIHQTESSLQGLGMACGVARSSQPLRWQHEDKSGIIHPFVIPTLPFTLWGRDIMKDIKVRLMTDSPDDSQDL

gag-pro-pol

MIGAIESNLFADQISWKSDQPVWLNQWPLKQEKLQALQQLVTEQLQLGHLEESNSPWNTPVFVIKKKSGKWRLLQDLRAVNATMHDMGALQPGLPSPVAVPKGWEIIIIDLQDCFFNIKLHPEDCKRFAFSVPSPNFKRPYQRFQWKVLPQGMKNSPTLCQKFVDKAILTVRDKYQDSYIVHYMDDILLAHPSRSIVDEILTSMIQALNKHGLVVSTEKIQKYDNLKYLGTHIQGDSVSYQKLQIRTDKLRTLNDFQKLLGNINWIRPFLKLTTGELKPLFEILNGDSNPISTRKLTPEACKALQLMNERLSTARVKRLDLSQPWSLCILKTEYTPTACLWQDGVVEWIHLPHISPKVITPYDIFCTQLIIKGRHRSKELFSKDPDYIVVPYTKVQFDLLLQEKEDWPISLLGFLGEVHFHLPKDPLLTFTLQTAIIFPHMTSTTPLEKGIVIFTDGSANGRSVTYIQGREPIIKENTQNTAQQAEIVAVITAFEEVSQPFNLYTDSKYVTGLFPEIETATLSPRTKIYTELKHLQRLIHKRQEKFYIGHIRGHTGLPGPLAQGNAYADSLTRILTALESAQESHALHHQNAAALRFQFHITREQAREIVKLCPNCPDWGHAPQLGVNPRGLKPRVLWQMDVTHVSEFGKLKYVHVTVDTYSHFTFATARTGEATKDVLQHLAQSFAYMGIPQKIKTDNAPAYVSRSIQEFLARWKISHVTGIPYNPQGQAIVERTHQNIKAQLNKLQKAGKYYTPHHLLAHALFVLNHVNMDNQGHTAAERHWGPISADPKPMVMWKDLLTGSWKGPDVLITAGRGYACVFPQDAETPIWVPDRFIRPFTERKEATPTPGTAEKTPPRDEKDQQESPKNESSPHQREDGLATSAGVDLRSGGGP*

.....................................................NSPWNSPILIIKKKSGKWRLLQDLRAISETMQDMGVLQPGX.............XIDLQDCFFNIPLDPKDRPRFAFSLPSENLRRPYQRFQWKVLPQGMKNSPTLCQKFVDMALMQVRQK..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

env

MPKHQSGSPTDSSDLLLSGKKQRPHLALRRKRRREMRKINRKVPRMNLVPIKEKTAWQHLQALISEAEEVLKTSQTPQTSLTLFLALLSVLGPPPVTGESYWAYLPKPPILHPVGWGSTDPIRVLTNQTMYLGGSPDFHGFRNMSGNVHFEGKSDTLPICLSFSFSTPTGCFQVDKQVFLSDTPTVDNNKPGGKGDKRRMWELWLTTLGNSGANTKLVPIKKKLPPKYPHCQIAFKKDAFWEGDESAPPRWLPCAFPDQGVSFSPKGALGLLWDFSLPSPSVDQSDQIKSKKNLFGNYTPPVNKEVHRWYEAGWVEPTWFWENSPKDPNDRDFTALVPHTELFRLVAASRHLILKRPGFQEHEMIPTSACVTYPYAILLGLPQLIDIEKRGSTFHISCSSCRLTNCLDSSAYDYAAIIVKRPPYVLLPVDIGDEPWFDDSAIQTFRYATDLIRAKRFVAAIILGISALIAIITSFAVATTALVKEMQTATFVNNLHRNVTLALSEQRIIDLKLEARLNALEEVVLELGQDVANLKTRMSTRCHANYDFICVTPLPYNATENWERTRAHLLGIWNDNEISYNIQELTNLISDMSKQHIDAVDLSGLAQSFANGVKALNPLDWTQYFIFIGVGALLLVIVLMIFPIVFQCLAKSLDQVQSDLNVLLLKKKKGGNAAPAAEMVELPRVSYT*

SAG

MPRLQQKWLNSRECPTLRGEAAKGLFPTKDDPSAHKRMSPSDKDILILCCKLGIALLCLGLLGEVAVRARRALTLDSFNSSSVQDYNLNDSENSTFLLRQGPQPTSSYKPHQPCPSEIEIRMLAKNYIFTNKTNPIGRLLVTMLRNESLPFSTIFTQIQRLEMGIENRKRHSTSVEEQVQGLRASGLEVKRGKRSALVKIGDRWWQPGTYRGPYIYRPTDAPLPYTGRYDLNFDRWVTVNGYKVLYRSLSFRERLARARPPWCMLTQEEKNDMKQQVHDYIYLGTGMSSIWGKIFHTKERTVAALIEHYSAKTYGMSYYD*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	1672	3412	6.7%	296	25.6%	584 (98.5%)	375 (63.2%)	6/3
Mutations:	1674G>A 1677G>C 1679G>T 1680G>T 1689A>T 1693T>G 1695A>T 1696T>C 1697T>C 1698G>T 1701T>C 1704G>A 1705G>A 1706A>C 1707T>A 1710C>G 1711A>T 1713C>G 1716C>A 1722A>T 1725T>A 1728A>G 1729A>T 1730C>T 1731A>T 1734A>G 1735A>T 1737T>A 1738A>C 1741C>A 1742A>C 1743G>A 1746T>C 1749T>C 1753C>A 1754G>A 1755T>A 1756G>C 1757C>A 1758T>A 1762C>G 1763T>C 1764G>T 1768G>T 1769C>T 1771T>A 1773T>G 1776C>A 1779A>C 1780G>T 1782T>C 1783G>A 1785T>G 1788G>A 1791T>A 1792A>G 1794G>T 1797A>C 1798T>A 1799A>T 1800T>G 1806A>C 1810A>T 1812G>A 1814G>A 1818A>G 1819C>G 1823A>G 1824G>C 1825_1827delTAT 1828T>C 1831A>C 1832C>T 1833C>T 1835T>A 1837G>T 1838T>G 1839A>T 1841A>T 1848A>T 1849T>A 1850A>T 1851T>G 1852G>A 1853G>C 1855G>A 1856G>A 1857_1858insAAA 1863A>T 1864G>A 1868G>C 1870C>G 1871A>T 1872A>G 1873G>A 1877C>T 1881A>T 1884G>T 1885C>G 1886C>A 1887_1888insAAT 1889T>C 1890T>C 1893T>C 1899C>T 1905T>A 1906A>C 1908G>A 1909A>C 1910C>A 1911A>G 1918A>T 1920C>T 1923A>T 1925A>G 1927G>C 1929C>A 1932T>C 1933A>C 1934A>C 1935G>C 3055C>T 3064T>C 3065A>T 3067G>T 3070T>C 3071G>A 3074T>C 3076T>C 3077G>A 3079C>T 3082T>C 3091G>A 3094A>T 3107C>T 3118C>T 3121A>G 3122C>A 3124T>A 3127A>C 3128G>A 3132A>G 3135C>A 3136T>G 3139A>C 3145C>A 3154A>G 3156C>T 3157A>C 3158T>C 3214A>T 3221C>T 3223A>G 3229T>C 3232C>T 3238T>C 3241T>C 3244A>C 3245A>C 3246A>C 3247A>C 3248C>T 3250G>A 3251C>G 3253T>C 3257G>A 3259A>G 3262T>C 3263T>A 3265T>G 3266A>C 3267A>C 3268A>C 3269A>C 3277T>C 3283T>C 3284G>T 3286G>A 3289C>T 3292C>A 3293C>G 3294C>A 3295T>A 3298T>C 3301T>G 3303A>G 3316A>G 3322C>T 3325A>G 3334T>G 3335T>C 3340C>G 3343G>A 3346T>A 3355T>C 3361T>A 3364T>G 3367A>G 3370T>C 3382G>T 3385C>T 3387A>T 3388A>G 3391T>C 3392A>T 3395T>A 3398A>C 3399C>A 3400T>G 3403A>C 3407G>C 3409T>A
CDS

gag-pro-pol	454	1034	11.2%	986	68.1%	195 (98.5%)	124 (62.6%)	2/1/0/0	0
Protein mutations:	W456F (1679G>T 1680G>T) S461A (1693T>G 1695A>T) L462P (1696T>C 1697T>C 1698G>T) D465T (1705G>A 1706A>C 1707T>A) I467L (1711A>T 1713C>G) T473F (1729A>T 1730C>T 1731A>T) T475S (1735A>T 1737T>A) I476L (1738A>C) Q477T (1741C>A 1742A>C 1743G>A) R481K (1753C>A 1754G>A 1755T>A) A482Q (1756G>C 1757C>A 1758T>A) L484A (1762C>G 1763T>C 1764G>T) A486F (1768G>T 1769C>T) S487T (1771T>A 1773T>G) V490F (1780G>T 1782T>C) V491M (1783G>A 1785T>G) M494V (1792A>G 1794G>T) Y496M (1798T>A 1799A>T 1800T>G) M500L (1810A>T 1812G>A) R501K (1814G>A) Q503E (1819C>G) K504S (1823A>G 1824G>C) Y505del (1825_1827delTAT) S506P (1828T>C) T507L (1831A>C 1832C>T 1833C>T) F508Y (1835T>A) V509C (1837G>T 1838T>G 1839A>T) K510M (1841A>T) Y513M (1849T>A 1850A>T 1851T>G) G514T (1852G>A 1853G>C) G515K (1855G>A 1856G>A) G515_G516insK (1857_1858insAAA) K517N (1863A>T) G518R (1864G>A) G519A (1868G>C) Q520V (1870C>G 1871A>T 1872A>G) G521R (1873G>A) A522V (1877C>T) E523D (1881A>T) P525E (1885C>G 1886C>A) P525_V526insN (1887_1888insAAT) V526A (1889T>C 1890T>C) K532Q (1906A>C 1908G>A) T533Q (1909A>C 1910C>A 1911A>G) I536F (1918A>T 1920C>T) R537S (1923A>T) K538R (1925A>G) D539Q (1927G>C 1929C>A) K541P (1933A>C 1934A>C 1935G>C) T919S (3065A>T 3067G>T) V921I (3071G>A) F922L (3074T>C 3076T>C) V923I (3077G>A 3079C>T) V940I (3128G>A) N941S (3132A>G) A942E (3135C>A 3136T>G) H945Q (3145C>A) A949V (3156C>T 3157A>C) K979P (3245A>C 3246A>C 3247A>C) H981D (3251C>G 3253T>C) E983K (3257G>A 3259A>G) C985R (3263T>A 3265T>G) K986P (3266A>C 3267A>C 3268A>C) V992L (3284G>T 3286G>A) P995E (3293C>G 3294C>A 3295T>A) F997L (3301T>G) K998R (3303A>G) K1026M (3387A>T 3388A>G) I1028L (3392A>T) L1029M (3395T>A) T1030Q (3398A>C 3399C>A 3400T>G) D1033Q (3407G>C 3409T>A)
Codon mutations:	TTG454TTA (1674G>A) GCG455GCC (1677G>C) TGG456TTT (1679G>T 1680G>T) GCA459GCT (1689A>T) TCA461GCT (1693T>G 1695A>T) TTG462CCT (1696T>C 1697T>C 1698G>T) TGT463TGC (1701T>C) CAG464CAA (1704G>A) GAT465ACA (1705G>A 1706A>C 1707T>A) CTC466CTG (1710C>G) ATC467TTG (1711A>T 1713C>G) CGC468CGA (1716C>A) ATA470ATT (1722A>T) CGT471CGA (1725T>A) AAA472AAG (1728A>G) ACA473TTT (1729A>T 1730C>T 1731A>T) GGA474GGG (1734A>G) ACT475TCA (1735A>T 1737T>A) ATA476CTA (1738A>C) CAG477ACA (1741C>A 1742A>C 1743G>A) GAT478GAC (1746T>C) TAT479TAC (1749T>C) CGT481AAA (1753C>A 1754G>A 1755T>A) GCT482CAA (1756G>C 1757C>A 1758T>A) CTG484GCT (1762C>G 1763T>C 1764G>T) GCT486TTT (1768G>T 1769C>T) TCT487ACG (1771T>A 1773T>G) CCC488CCA (1776C>A) GCA489GCC (1779A>C) GTT490TTC (1780G>T 1782T>C) GTT491ATG (1783G>A 1785T>G) CAG492CAA (1788G>A) GGT493GGA (1791T>A) ATG494GTT (1792A>G 1794G>T) GCA495GCC (1797A>C) TAT496ATG (1798T>A 1799A>T 1800T>G) GCA498GCC (1806A>C) ATG500TTA (1810A>T 1812G>A) AGA501AAA (1814G>A) GGA502GGG (1818A>G) CAA503GAA (1819C>G) AAG504AGC (1823A>G 1824G>C) TAT505del (1825_1827delTAT) TCT506CCT (1828T>C) ACC507CTT (1831A>C 1832C>T 1833C>T) TTT508TAT (1835T>A) GTA509TGT (1837G>T 1838T>G 1839A>T) AAG510ATG (1841A>T) ACA512ACT (1848A>T) TAT513ATG (1849T>A 1850A>T 1851T>G) GGT514ACT (1852G>A 1853G>C) GGG515AAG (1855G>A 1856G>A) GGG515_GGA516insAAA (1857_1858insAAA) AAA517AAT (1863A>T) GGA518AGA (1864G>A) GGT519GCT (1868G>C) CAA520GTG (1870C>G 1871A>T 1872A>G) GGA521AGA (1873G>A) GCA522GTA (1877C>T) GAA523GAT (1881A>T) GGG524GGT (1884G>T) CCA525GAA (1885C>G 1886C>A) CCA525_GTT526insAAT (1887_1888insAAT) GTT526GCC (1889T>C 1890T>C) TGT527TGC (1893T>C) TCC529TCT (1899C>T) GGT531GGA (1905T>A) AAG532CAA (1906A>C 1908G>A) ACA533CAG (1909A>C 1910C>A 1911A>G) ATC536TTT (1918A>T 1920C>T) AGA537AGT (1923A>T) AAA538AGA (1925A>G) GAC539CAA (1927G>C 1929C>A) TGT540TGC (1932T>C) AAG541CCC (1933A>C 1934A>C 1935G>C) AGC915AGT (3055C>T) AAT918AAC (3064T>C) ACG919TCT (3065A>T 3067G>T) CCT920CCC (3070T>C) GTT921ATT (3071G>A) TTT922CTC (3074T>C 3076T>C) GTC923ATT (3077G>A 3079C>T) ATT924ATC (3082T>C) AAG927AAA (3091G>A) TCA928TCT (3094A>T) CTG933TTG (3107C>T) GAC936GAT (3118C>T) CTA937CTG (3121A>G) CGT938AGA (3122C>A 3124T>A) GCA939GCC (3127A>C) GTT940ATT (3128G>A) AAT941AGT (3132A>G) GCT942GAG (3135C>A 3136T>G) ACA943ACC (3139A>C) CAC945CAA (3145C>A) GGA948GGG (3154A>G) GCA949GTC (3156C>T 3157A>C) TTA950CTA (3158T>C) ATA968.TT (3214A>T) CTA971TTG (3221C>T 3223A>G) GAT973GAC (3229T>C) TGC974TGT (3232C>T) TTT976TTC (3238T>C) AAT977AAC (3241T>C) ATA978ATC (3244A>C) AAA979CCC (3245A>C 3246A>C 3247A>C) CTG980TTA (3248C>T 3250G>A) CAT981GAC (3251C>G 3253T>C) GAA983AAG (3257G>A 3259A>G) GAT984GAC (3262T>C) TGT985AGG (3263T>A 3265T>G) AAA986CCC (3266A>C 3267A>C 3268A>C) AGA987CGA (3269A>C) GCT989GCC (3277T>C) AGT991AGC (3283T>C) GTG992TTA (3284G>T 3286G>A) CCC993CCT (3289C>T) TCC994TCA (3292C>A) CCT995GAA (3293C>G 3294C>A 3295T>A) AAT996AAC (3298T>C) TTT997TTG (3301T>G) AAG998AGG (3303A>G) CAA1002CAG (3316A>G) TTC1004TTT (3322C>T) CAA1005CAG (3325A>G) GTT1008GTG (3334T>G) TTG1009CTG (3335T>C) CCC1010CCG (3340C>G) CAG1011CAA (3343G>A) GGT1012GGA (3346T>A) AAT1015AAC (3355T>C) CCT1017CCA (3361T>A) ACT1018ACG (3364T>G) TTA1019TTG (3367A>G) TGT1020TGC (3370T>C) GTG1024GTT (3382G>T) GAC1025GAT (3385C>T) AAA1026ATG (3387A>T 3388A>G) GCT1027GCC (3391T>C) ATA1028TTA (3392A>T) TTG1029ATG (3395T>A) ACT1030CAG (3398A>C 3399C>A 3400T>G) GTA1031GTC (3403A>C) GAT1033CAA (3407G>C 3409T>A)
gag-pro	454	542	10.3%	321	50.4%	88 (96.7%)	41 (45.1%)	2/1/0/0	0
Protein mutations:	W456F (1679G>T 1680G>T) S461A (1693T>G 1695A>T) L462P (1696T>C 1697T>C 1698G>T) D465T (1705G>A 1706A>C 1707T>A) I467L (1711A>T 1713C>G) T473F (1729A>T 1730C>T 1731A>T) T475S (1735A>T 1737T>A) I476L (1738A>C) Q477T (1741C>A 1742A>C 1743G>A) R481K (1753C>A 1754G>A 1755T>A) A482Q (1756G>C 1757C>A 1758T>A) L484A (1762C>G 1763T>C 1764G>T) A486F (1768G>T 1769C>T) S487T (1771T>A 1773T>G) V490F (1780G>T 1782T>C) V491M (1783G>A 1785T>G) M494V (1792A>G 1794G>T) Y496M (1798T>A 1799A>T 1800T>G) M500L (1810A>T 1812G>A) R501K (1814G>A) Q503E (1819C>G) K504S (1823A>G 1824G>C) Y505del (1825_1827delTAT) S506P (1828T>C) T507L (1831A>C 1832C>T 1833C>T) F508Y (1835T>A) V509C (1837G>T 1838T>G 1839A>T) K510M (1841A>T) Y513M (1849T>A 1850A>T 1851T>G) G514T (1852G>A 1853G>C) G515K (1855G>A 1856G>A) G515_G516insK (1857_1858insAAA) K517N (1863A>T) G518R (1864G>A) G519A (1868G>C) Q520V (1870C>G 1871A>T 1872A>G) G521R (1873G>A) A522V (1877C>T) E523D (1881A>T) P525E (1885C>G 1886C>A) P525_V526insN (1887_1888insAAT) V526A (1889T>C 1890T>C) K532Q (1906A>C 1908G>A) T533Q (1909A>C 1910C>A 1911A>G) I536F (1918A>T 1920C>T) R537S (1923A>T) K538R (1925A>G) D539Q (1927G>C 1929C>A) K541P (1933A>C 1934A>C 1935G>C)
Codon mutations:	TTG454TTA (1674G>A) GCG455GCC (1677G>C) TGG456TTT (1679G>T 1680G>T) GCA459GCT (1689A>T) TCA461GCT (1693T>G 1695A>T) TTG462CCT (1696T>C 1697T>C 1698G>T) TGT463TGC (1701T>C) CAG464CAA (1704G>A) GAT465ACA (1705G>A 1706A>C 1707T>A) CTC466CTG (1710C>G) ATC467TTG (1711A>T 1713C>G) CGC468CGA (1716C>A) ATA470ATT (1722A>T) CGT471CGA (1725T>A) AAA472AAG (1728A>G) ACA473TTT (1729A>T 1730C>T 1731A>T) GGA474GGG (1734A>G) ACT475TCA (1735A>T 1737T>A) ATA476CTA (1738A>C) CAG477ACA (1741C>A 1742A>C 1743G>A) GAT478GAC (1746T>C) TAT479TAC (1749T>C) CGT481AAA (1753C>A 1754G>A 1755T>A) GCT482CAA (1756G>C 1757C>A 1758T>A) CTG484GCT (1762C>G 1763T>C 1764G>T) GCT486TTT (1768G>T 1769C>T) TCT487ACG (1771T>A 1773T>G) CCC488CCA (1776C>A) GCA489GCC (1779A>C) GTT490TTC (1780G>T 1782T>C) GTT491ATG (1783G>A 1785T>G) CAG492CAA (1788G>A) GGT493GGA (1791T>A) ATG494GTT (1792A>G 1794G>T) GCA495GCC (1797A>C) TAT496ATG (1798T>A 1799A>T 1800T>G) GCA498GCC (1806A>C) ATG500TTA (1810A>T 1812G>A) AGA501AAA (1814G>A) GGA502GGG (1818A>G) CAA503GAA (1819C>G) AAG504AGC (1823A>G 1824G>C) TAT505del (1825_1827delTAT) TCT506CCT (1828T>C) ACC507CTT (1831A>C 1832C>T 1833C>T) TTT508TAT (1835T>A) GTA509TGT (1837G>T 1838T>G 1839A>T) AAG510ATG (1841A>T) ACA512ACT (1848A>T) TAT513ATG (1849T>A 1850A>T 1851T>G) GGT514ACT (1852G>A 1853G>C) GGG515AAG (1855G>A 1856G>A) GGG515_GGA516insAAA (1857_1858insAAA) AAA517AAT (1863A>T) GGA518AGA (1864G>A) GGT519GCT (1868G>C) CAA520GTG (1870C>G 1871A>T 1872A>G) GGA521AGA (1873G>A) GCA522GTA (1877C>T) GAA523GAT (1881A>T) GGG524GGT (1884G>T) CCA525GAA (1885C>G 1886C>A) CCA525_GTT526insAAT (1887_1888insAAT) GTT526GCC (1889T>C 1890T>C) TGT527TGC (1893T>C) TCC529TCT (1899C>T) GGT531GGA (1905T>A) AAG532CAA (1906A>C 1908G>A) ACA533CAG (1909A>C 1910C>A 1911A>G) ATC536TTT (1918A>T 1920C>T) AGA537AGT (1923A>T) AAA538AGA (1925A>G) GAC539CAA (1927G>C 1929C>A) TGT540TGC (1932T>C) AAG541CCC (1933A>C 1934A>C 1935G>C)
gag	454	542	15.0%	321	50.4%	88 (96.7%)	41 (45.1%)	2/1/0/0	0
Protein mutations:	W456F (1679G>T 1680G>T) S461A (1693T>G 1695A>T) L462P (1696T>C 1697T>C 1698G>T) D465T (1705G>A 1706A>C 1707T>A) I467L (1711A>T 1713C>G) T473F (1729A>T 1730C>T 1731A>T) T475S (1735A>T 1737T>A) I476L (1738A>C) Q477T (1741C>A 1742A>C 1743G>A) R481K (1753C>A 1754G>A 1755T>A) A482Q (1756G>C 1757C>A 1758T>A) L484A (1762C>G 1763T>C 1764G>T) A486F (1768G>T 1769C>T) S487T (1771T>A 1773T>G) V490F (1780G>T 1782T>C) V491M (1783G>A 1785T>G) M494V (1792A>G 1794G>T) Y496M (1798T>A 1799A>T 1800T>G) M500L (1810A>T 1812G>A) R501K (1814G>A) Q503E (1819C>G) K504S (1823A>G 1824G>C) Y505del (1825_1827delTAT) S506P (1828T>C) T507L (1831A>C 1832C>T 1833C>T) F508Y (1835T>A) V509C (1837G>T 1838T>G 1839A>T) K510M (1841A>T) Y513M (1849T>A 1850A>T 1851T>G) G514T (1852G>A 1853G>C) G515K (1855G>A 1856G>A) G515_G516insK (1857_1858insAAA) K517N (1863A>T) G518R (1864G>A) G519A (1868G>C) Q520V (1870C>G 1871A>T 1872A>G) G521R (1873G>A) A522V (1877C>T) E523D (1881A>T) P525E (1885C>G 1886C>A) P525_V526insN (1887_1888insAAT) V526A (1889T>C 1890T>C) K532Q (1906A>C 1908G>A) T533Q (1909A>C 1910C>A 1911A>G) I536F (1918A>T 1920C>T) R537S (1923A>T) K538R (1925A>G) D539Q (1927G>C 1929C>A) K541P (1933A>C 1934A>C 1935G>C)
Codon mutations:	TTG454TTA (1674G>A) GCG455GCC (1677G>C) TGG456TTT (1679G>T 1680G>T) GCA459GCT (1689A>T) TCA461GCT (1693T>G 1695A>T) TTG462CCT (1696T>C 1697T>C 1698G>T) TGT463TGC (1701T>C) CAG464CAA (1704G>A) GAT465ACA (1705G>A 1706A>C 1707T>A) CTC466CTG (1710C>G) ATC467TTG (1711A>T 1713C>G) CGC468CGA (1716C>A) ATA470ATT (1722A>T) CGT471CGA (1725T>A) AAA472AAG (1728A>G) ACA473TTT (1729A>T 1730C>T 1731A>T) GGA474GGG (1734A>G) ACT475TCA (1735A>T 1737T>A) ATA476CTA (1738A>C) CAG477ACA (1741C>A 1742A>C 1743G>A) GAT478GAC (1746T>C) TAT479TAC (1749T>C) CGT481AAA (1753C>A 1754G>A 1755T>A) GCT482CAA (1756G>C 1757C>A 1758T>A) CTG484GCT (1762C>G 1763T>C 1764G>T) GCT486TTT (1768G>T 1769C>T) TCT487ACG (1771T>A 1773T>G) CCC488CCA (1776C>A) GCA489GCC (1779A>C) GTT490TTC (1780G>T 1782T>C) GTT491ATG (1783G>A 1785T>G) CAG492CAA (1788G>A) GGT493GGA (1791T>A) ATG494GTT (1792A>G 1794G>T) GCA495GCC (1797A>C) TAT496ATG (1798T>A 1799A>T 1800T>G) GCA498GCC (1806A>C) ATG500TTA (1810A>T 1812G>A) AGA501AAA (1814G>A) GGA502GGG (1818A>G) CAA503GAA (1819C>G) AAG504AGC (1823A>G 1824G>C) TAT505del (1825_1827delTAT) TCT506CCT (1828T>C) ACC507CTT (1831A>C 1832C>T 1833C>T) TTT508TAT (1835T>A) GTA509TGT (1837G>T 1838T>G 1839A>T) AAG510ATG (1841A>T) ACA512ACT (1848A>T) TAT513ATG (1849T>A 1850A>T 1851T>G) GGT514ACT (1852G>A 1853G>C) GGG515AAG (1855G>A 1856G>A) GGG515_GGA516insAAA (1857_1858insAAA) AAA517AAT (1863A>T) GGA518AGA (1864G>A) GGT519GCT (1868G>C) CAA520GTG (1870C>G 1871A>T 1872A>G) GGA521AGA (1873G>A) GCA522GTA (1877C>T) GAA523GAT (1881A>T) GGG524GGT (1884G>T) CCA525GAA (1885C>G 1886C>A) CCA525_GTT526insAAT (1887_1888insAAT) GTT526GCC (1889T>C 1890T>C) TGT527TGC (1893T>C) TCC529TCT (1899C>T) GGT531GGA (1905T>A) AAG532CAA (1906A>C 1908G>A) ACA533CAG (1909A>C 1910C>A 1911A>G) ATC536TTT (1918A>T 1920C>T) AGA537AGT (1923A>T) AAA538AGA (1925A>G) GAC539CAA (1927G>C 1929C>A) TGT540TGC (1932T>C) AAG541CCC (1933A>C 1934A>C 1935G>C)
Proteins

Pr160 (NP_056880.1)	454	1034	11.2%	986	68.1%	195 (98.5%)	124 (62.6%)	2/1/0/0	0
Protein mutations:	W456F (1679G>T 1680G>T) S461A (1693T>G 1695A>T) L462P (1696T>C 1697T>C 1698G>T) D465T (1705G>A 1706A>C 1707T>A) I467L (1711A>T 1713C>G) T473F (1729A>T 1730C>T 1731A>T) T475S (1735A>T 1737T>A) I476L (1738A>C) Q477T (1741C>A 1742A>C 1743G>A) R481K (1753C>A 1754G>A 1755T>A) A482Q (1756G>C 1757C>A 1758T>A) L484A (1762C>G 1763T>C 1764G>T) A486F (1768G>T 1769C>T) S487T (1771T>A 1773T>G) V490F (1780G>T 1782T>C) V491M (1783G>A 1785T>G) M494V (1792A>G 1794G>T) Y496M (1798T>A 1799A>T 1800T>G) M500L (1810A>T 1812G>A) R501K (1814G>A) Q503E (1819C>G) K504S (1823A>G 1824G>C) Y505del (1825_1827delTAT) S506P (1828T>C) T507L (1831A>C 1832C>T 1833C>T) F508Y (1835T>A) V509C (1837G>T 1838T>G 1839A>T) K510M (1841A>T) Y513M (1849T>A 1850A>T 1851T>G) G514T (1852G>A 1853G>C) G515K (1855G>A 1856G>A) G515_G516insK (1857_1858insAAA) K517N (1863A>T) G518R (1864G>A) G519A (1868G>C) Q520V (1870C>G 1871A>T 1872A>G) G521R (1873G>A) A522V (1877C>T) E523D (1881A>T) P525E (1885C>G 1886C>A) P525_V526insN (1887_1888insAAT) V526A (1889T>C 1890T>C) K532Q (1906A>C 1908G>A) T533Q (1909A>C 1910C>A 1911A>G) I536F (1918A>T 1920C>T) R537S (1923A>T) K538R (1925A>G) D539Q (1927G>C 1929C>A) K541P (1933A>C 1934A>C 1935G>C) T919S (3065A>T 3067G>T) V921I (3071G>A) F922L (3074T>C 3076T>C) V923I (3077G>A 3079C>T) V940I (3128G>A) N941S (3132A>G) A942E (3135C>A 3136T>G) H945Q (3145C>A) A949V (3156C>T 3157A>C) K979P (3245A>C 3246A>C 3247A>C) H981D (3251C>G 3253T>C) E983K (3257G>A 3259A>G) C985R (3263T>A 3265T>G) K986P (3266A>C 3267A>C 3268A>C) V992L (3284G>T 3286G>A) P995E (3293C>G 3294C>A 3295T>A) F997L (3301T>G) K998R (3303A>G) K1026M (3387A>T 3388A>G) I1028L (3392A>T) L1029M (3395T>A) T1030Q (3398A>C 3399C>A 3400T>G) D1033Q (3407G>C 3409T>A)
Codon mutations:	TTG454TTA (1674G>A) GCG455GCC (1677G>C) TGG456TTT (1679G>T 1680G>T) GCA459GCT (1689A>T) TCA461GCT (1693T>G 1695A>T) TTG462CCT (1696T>C 1697T>C 1698G>T) TGT463TGC (1701T>C) CAG464CAA (1704G>A) GAT465ACA (1705G>A 1706A>C 1707T>A) CTC466CTG (1710C>G) ATC467TTG (1711A>T 1713C>G) CGC468CGA (1716C>A) ATA470ATT (1722A>T) CGT471CGA (1725T>A) AAA472AAG (1728A>G) ACA473TTT (1729A>T 1730C>T 1731A>T) GGA474GGG (1734A>G) ACT475TCA (1735A>T 1737T>A) ATA476CTA (1738A>C) CAG477ACA (1741C>A 1742A>C 1743G>A) GAT478GAC (1746T>C) TAT479TAC (1749T>C) CGT481AAA (1753C>A 1754G>A 1755T>A) GCT482CAA (1756G>C 1757C>A 1758T>A) CTG484GCT (1762C>G 1763T>C 1764G>T) GCT486TTT (1768G>T 1769C>T) TCT487ACG (1771T>A 1773T>G) CCC488CCA (1776C>A) GCA489GCC (1779A>C) GTT490TTC (1780G>T 1782T>C) GTT491ATG (1783G>A 1785T>G) CAG492CAA (1788G>A) GGT493GGA (1791T>A) ATG494GTT (1792A>G 1794G>T) GCA495GCC (1797A>C) TAT496ATG (1798T>A 1799A>T 1800T>G) GCA498GCC (1806A>C) ATG500TTA (1810A>T 1812G>A) AGA501AAA (1814G>A) GGA502GGG (1818A>G) CAA503GAA (1819C>G) AAG504AGC (1823A>G 1824G>C) TAT505del (1825_1827delTAT) TCT506CCT (1828T>C) ACC507CTT (1831A>C 1832C>T 1833C>T) TTT508TAT (1835T>A) GTA509TGT (1837G>T 1838T>G 1839A>T) AAG510ATG (1841A>T) ACA512ACT (1848A>T) TAT513ATG (1849T>A 1850A>T 1851T>G) GGT514ACT (1852G>A 1853G>C) GGG515AAG (1855G>A 1856G>A) GGG515_GGA516insAAA (1857_1858insAAA) AAA517AAT (1863A>T) GGA518AGA (1864G>A) GGT519GCT (1868G>C) CAA520GTG (1870C>G 1871A>T 1872A>G) GGA521AGA (1873G>A) GCA522GTA (1877C>T) GAA523GAT (1881A>T) GGG524GGT (1884G>T) CCA525GAA (1885C>G 1886C>A) CCA525_GTT526insAAT (1887_1888insAAT) GTT526GCC (1889T>C 1890T>C) TGT527TGC (1893T>C) TCC529TCT (1899C>T) GGT531GGA (1905T>A) AAG532CAA (1906A>C 1908G>A) ACA533CAG (1909A>C 1910C>A 1911A>G) ATC536TTT (1918A>T 1920C>T) AGA537AGT (1923A>T) AAA538AGA (1925A>G) GAC539CAA (1927G>C 1929C>A) TGT540TGC (1932T>C) AAG541CCC (1933A>C 1934A>C 1935G>C) AGC915AGT (3055C>T) AAT918AAC (3064T>C) ACG919TCT (3065A>T 3067G>T) CCT920CCC (3070T>C) GTT921ATT (3071G>A) TTT922CTC (3074T>C 3076T>C) GTC923ATT (3077G>A 3079C>T) ATT924ATC (3082T>C) AAG927AAA (3091G>A) TCA928TCT (3094A>T) CTG933TTG (3107C>T) GAC936GAT (3118C>T) CTA937CTG (3121A>G) CGT938AGA (3122C>A 3124T>A) GCA939GCC (3127A>C) GTT940ATT (3128G>A) AAT941AGT (3132A>G) GCT942GAG (3135C>A 3136T>G) ACA943ACC (3139A>C) CAC945CAA (3145C>A) GGA948GGG (3154A>G) GCA949GTC (3156C>T 3157A>C) TTA950CTA (3158T>C) ATA968.TT (3214A>T) CTA971TTG (3221C>T 3223A>G) GAT973GAC (3229T>C) TGC974TGT (3232C>T) TTT976TTC (3238T>C) AAT977AAC (3241T>C) ATA978ATC (3244A>C) AAA979CCC (3245A>C 3246A>C 3247A>C) CTG980TTA (3248C>T 3250G>A) CAT981GAC (3251C>G 3253T>C) GAA983AAG (3257G>A 3259A>G) GAT984GAC (3262T>C) TGT985AGG (3263T>A 3265T>G) AAA986CCC (3266A>C 3267A>C 3268A>C) AGA987CGA (3269A>C) GCT989GCC (3277T>C) AGT991AGC (3283T>C) GTG992TTA (3284G>T 3286G>A) CCC993CCT (3289C>T) TCC994TCA (3292C>A) CCT995GAA (3293C>G 3294C>A 3295T>A) AAT996AAC (3298T>C) TTT997TTG (3301T>G) AAG998AGG (3303A>G) CAA1002CAG (3316A>G) TTC1004TTT (3322C>T) CAA1005CAG (3325A>G) GTT1008GTG (3334T>G) TTG1009CTG (3335T>C) CCC1010CCG (3340C>G) CAG1011CAA (3343G>A) GGT1012GGA (3346T>A) AAT1015AAC (3355T>C) CCT1017CCA (3361T>A) ACT1018ACG (3364T>G) TTA1019TTG (3367A>G) TGT1020TGC (3370T>C) GTG1024GTT (3382G>T) GAC1025GAT (3385C>T) AAA1026ATG (3387A>T 3388A>G) GCT1027GCC (3391T>C) ATA1028TTA (3392A>T) TTG1029ATG (3395T>A) ACT1030CAG (3398A>C 3399C>A 3400T>G) GTA1031GTC (3403A>C) GAT1033CAA (3407G>C 3409T>A)
p30DU-p13PR-RT-IN (NP_955564.1)	170	290	10.6%	665	82.0%	107 (100%)	83 (77.6%)	0/0/0/0	0
Protein mutations:	T175S (3065A>T 3067G>T) V177I (3071G>A) F178L (3074T>C 3076T>C) V179I (3077G>A 3079C>T) V196I (3128G>A) N197S (3132A>G) A198E (3135C>A 3136T>G) H201Q (3145C>A) A205V (3156C>T 3157A>C) K235P (3245A>C 3246A>C 3247A>C) H237D (3251C>G 3253T>C) E239K (3257G>A 3259A>G) C241R (3263T>A 3265T>G) K242P (3266A>C 3267A>C 3268A>C) V248L (3284G>T 3286G>A) P251E (3293C>G 3294C>A 3295T>A) F253L (3301T>G) K254R (3303A>G) K282M (3387A>T 3388A>G) I284L (3392A>T) L285M (3395T>A) T286Q (3398A>C 3399C>A 3400T>G) D289Q (3407G>C 3409T>A)
Codon mutations:	AGC171AGT (3055C>T) AAT174AAC (3064T>C) ACG175TCT (3065A>T 3067G>T) CCT176CCC (3070T>C) GTT177ATT (3071G>A) TTT178CTC (3074T>C 3076T>C) GTC179ATT (3077G>A 3079C>T) ATT180ATC (3082T>C) AAG183AAA (3091G>A) TCA184TCT (3094A>T) CTG189TTG (3107C>T) GAC192GAT (3118C>T) CTA193CTG (3121A>G) CGT194AGA (3122C>A 3124T>A) GCA195GCC (3127A>C) GTT196ATT (3128G>A) AAT197AGT (3132A>G) GCT198GAG (3135C>A 3136T>G) ACA199ACC (3139A>C) CAC201CAA (3145C>A) GGA204GGG (3154A>G) GCA205GTC (3156C>T 3157A>C) TTA206CTA (3158T>C) ATA224.TT (3214A>T) CTA227TTG (3221C>T 3223A>G) GAT229GAC (3229T>C) TGC230TGT (3232C>T) TTT232TTC (3238T>C) AAT233AAC (3241T>C) ATA234ATC (3244A>C) AAA235CCC (3245A>C 3246A>C 3247A>C) CTG236TTA (3248C>T 3250G>A) CAT237GAC (3251C>G 3253T>C) GAA239AAG (3257G>A 3259A>G) GAT240GAC (3262T>C) TGT241AGG (3263T>A 3265T>G) AAA242CCC (3266A>C 3267A>C 3268A>C) AGA243CGA (3269A>C) GCT245GCC (3277T>C) AGT247AGC (3283T>C) GTG248TTA (3284G>T 3286G>A) CCC249CCT (3289C>T) TCC250TCA (3292C>A) CCT251GAA (3293C>G 3294C>A 3295T>A) AAT252AAC (3298T>C) TTT253TTG (3301T>G) AAG254AGG (3303A>G) CAA258CAG (3316A>G) TTC260TTT (3322C>T) CAA261CAG (3325A>G) GTT264GTG (3334T>G) TTG265CTG (3335T>C) CCC266CCG (3340C>G) CAG267CAA (3343G>A) GGT268GGA (3346T>A) AAT271AAC (3355T>C) CCT273CCA (3361T>A) ACT274ACG (3364T>G) TTA275TTG (3367A>G) TGT276TGC (3370T>C) GTG280GTT (3382G>T) GAC281GAT (3385C>T) AAA282ATG (3387A>T 3388A>G) GCT283GCC (3391T>C) ATA284TTA (3392A>T) TTG285ATG (3395T>A) ACT286CAG (3398A>C 3399C>A 3400T>G) GTA287GTC (3403A>C) GAT289CAA (3407G>C 3409T>A)
Pr110 (NP_056881.1)	454	542	10.3%	321	50.4%	88 (96.7%)	41 (45.1%)	2/1/0/0	0
Protein mutations:	W456F (1679G>T 1680G>T) S461A (1693T>G 1695A>T) L462P (1696T>C 1697T>C 1698G>T) D465T (1705G>A 1706A>C 1707T>A) I467L (1711A>T 1713C>G) T473F (1729A>T 1730C>T 1731A>T) T475S (1735A>T 1737T>A) I476L (1738A>C) Q477T (1741C>A 1742A>C 1743G>A) R481K (1753C>A 1754G>A 1755T>A) A482Q (1756G>C 1757C>A 1758T>A) L484A (1762C>G 1763T>C 1764G>T) A486F (1768G>T 1769C>T) S487T (1771T>A 1773T>G) V490F (1780G>T 1782T>C) V491M (1783G>A 1785T>G) M494V (1792A>G 1794G>T) Y496M (1798T>A 1799A>T 1800T>G) M500L (1810A>T 1812G>A) R501K (1814G>A) Q503E (1819C>G) K504S (1823A>G 1824G>C) Y505del (1825_1827delTAT) S506P (1828T>C) T507L (1831A>C 1832C>T 1833C>T) F508Y (1835T>A) V509C (1837G>T 1838T>G 1839A>T) K510M (1841A>T) Y513M (1849T>A 1850A>T 1851T>G) G514T (1852G>A 1853G>C) G515K (1855G>A 1856G>A) G515_G516insK (1857_1858insAAA) K517N (1863A>T) G518R (1864G>A) G519A (1868G>C) Q520V (1870C>G 1871A>T 1872A>G) G521R (1873G>A) A522V (1877C>T) E523D (1881A>T) P525E (1885C>G 1886C>A) P525_V526insN (1887_1888insAAT) V526A (1889T>C 1890T>C) K532Q (1906A>C 1908G>A) T533Q (1909A>C 1910C>A 1911A>G) I536F (1918A>T 1920C>T) R537S (1923A>T) K538R (1925A>G) D539Q (1927G>C 1929C>A) K541P (1933A>C 1934A>C 1935G>C)
Codon mutations:	TTG454TTA (1674G>A) GCG455GCC (1677G>C) TGG456TTT (1679G>T 1680G>T) GCA459GCT (1689A>T) TCA461GCT (1693T>G 1695A>T) TTG462CCT (1696T>C 1697T>C 1698G>T) TGT463TGC (1701T>C) CAG464CAA (1704G>A) GAT465ACA (1705G>A 1706A>C 1707T>A) CTC466CTG (1710C>G) ATC467TTG (1711A>T 1713C>G) CGC468CGA (1716C>A) ATA470ATT (1722A>T) CGT471CGA (1725T>A) AAA472AAG (1728A>G) ACA473TTT (1729A>T 1730C>T 1731A>T) GGA474GGG (1734A>G) ACT475TCA (1735A>T 1737T>A) ATA476CTA (1738A>C) CAG477ACA (1741C>A 1742A>C 1743G>A) GAT478GAC (1746T>C) TAT479TAC (1749T>C) CGT481AAA (1753C>A 1754G>A 1755T>A) GCT482CAA (1756G>C 1757C>A 1758T>A) CTG484GCT (1762C>G 1763T>C 1764G>T) GCT486TTT (1768G>T 1769C>T) TCT487ACG (1771T>A 1773T>G) CCC488CCA (1776C>A) GCA489GCC (1779A>C) GTT490TTC (1780G>T 1782T>C) GTT491ATG (1783G>A 1785T>G) CAG492CAA (1788G>A) GGT493GGA (1791T>A) ATG494GTT (1792A>G 1794G>T) GCA495GCC (1797A>C) TAT496ATG (1798T>A 1799A>T 1800T>G) GCA498GCC (1806A>C) ATG500TTA (1810A>T 1812G>A) AGA501AAA (1814G>A) GGA502GGG (1818A>G) CAA503GAA (1819C>G) AAG504AGC (1823A>G 1824G>C) TAT505del (1825_1827delTAT) TCT506CCT (1828T>C) ACC507CTT (1831A>C 1832C>T 1833C>T) TTT508TAT (1835T>A) GTA509TGT (1837G>T 1838T>G 1839A>T) AAG510ATG (1841A>T) ACA512ACT (1848A>T) TAT513ATG (1849T>A 1850A>T 1851T>G) GGT514ACT (1852G>A 1853G>C) GGG515AAG (1855G>A 1856G>A) GGG515_GGA516insAAA (1857_1858insAAA) AAA517AAT (1863A>T) GGA518AGA (1864G>A) GGT519GCT (1868G>C) CAA520GTG (1870C>G 1871A>T 1872A>G) GGA521AGA (1873G>A) GCA522GTA (1877C>T) GAA523GAT (1881A>T) GGG524GGT (1884G>T) CCA525GAA (1885C>G 1886C>A) CCA525_GTT526insAAT (1887_1888insAAT) GTT526GCC (1889T>C 1890T>C) TGT527TGC (1893T>C) TCC529TCT (1899C>T) GGT531GGA (1905T>A) AAG532CAA (1906A>C 1908G>A) ACA533CAG (1909A>C 1910C>A 1911A>G) ATC536TTT (1918A>T 1920C>T) AGA537AGT (1923A>T) AAA538AGA (1925A>G) GAC539CAA (1927G>C 1929C>A) TGT540TGC (1932T>C) AAG541CCC (1933A>C 1934A>C 1935G>C)
p14 NC (NP_955563.1)	1	46	18.5%	125	38.1%	45 (93.8%)	16 (33.3%)	2/1/0/0	0
Protein mutations:	M4L (1810A>T 1812G>A) R5K (1814G>A) Q7E (1819C>G) K8S (1823A>G 1824G>C) Y9del (1825_1827delTAT) S10P (1828T>C) T11L (1831A>C 1832C>T 1833C>T) F12Y (1835T>A) V13C (1837G>T 1838T>G 1839A>T) K14M (1841A>T) Y17M (1849T>A 1850A>T 1851T>G) G18T (1852G>A 1853G>C) G19K (1855G>A 1856G>A) G19_G20insK (1857_1858insAAA) K21N (1863A>T) G22R (1864G>A) G23A (1868G>C) Q24V (1870C>G 1871A>T 1872A>G) G25R (1873G>A) A26V (1877C>T) E27D (1881A>T) P29E (1885C>G 1886C>A) P29_V30insN (1887_1888insAAT) V30A (1889T>C 1890T>C) K36Q (1906A>C 1908G>A) T37Q (1909A>C 1910C>A 1911A>G) I40F (1918A>T 1920C>T) R41S (1923A>T) K42R (1925A>G) D43Q (1927G>C 1929C>A) K45P (1933A>C 1934A>C 1935G>C)
Codon mutations:	GCA2GCC (1806A>C) ATG4TTA (1810A>T 1812G>A) AGA5AAA (1814G>A) GGA6GGG (1818A>G) CAA7GAA (1819C>G) AAG8AGC (1823A>G 1824G>C) TAT9del (1825_1827delTAT) TCT10CCT (1828T>C) ACC11CTT (1831A>C 1832C>T 1833C>T) TTT12TAT (1835T>A) GTA13TGT (1837G>T 1838T>G 1839A>T) AAG14ATG (1841A>T) ACA16ACT (1848A>T) TAT17ATG (1849T>A 1850A>T 1851T>G) GGT18ACT (1852G>A 1853G>C) GGG19AAG (1855G>A 1856G>A) GGG19_GGA20insAAA (1857_1858insAAA) AAA21AAT (1863A>T) GGA22AGA (1864G>A) GGT23GCT (1868G>C) CAA24GTG (1870C>G 1871A>T 1872A>G) GGA25AGA (1873G>A) GCA26GTA (1877C>T) GAA27GAT (1881A>T) GGG28GGT (1884G>T) CCA29GAA (1885C>G 1886C>A) CCA29_GTT30insAAT (1887_1888insAAT) GTT30GCC (1889T>C 1890T>C) TGT31TGC (1893T>C) TCC33TCT (1899C>T) GGT35GGA (1905T>A) AAG36CAA (1906A>C 1908G>A) ACA37CAG (1909A>C 1910C>A 1911A>G) ATC40TTT (1918A>T 1920C>T) AGA41AGT (1923A>T) AAA42AGA (1925A>G) GAC43CAA (1927G>C 1929C>A) TGT44TGC (1932T>C) AAG45CCC (1933A>C 1934A>C 1935G>C)
Pr77 (NP_056882.1)	454	542	15.0%	321	50.4%	88 (96.7%)	41 (45.1%)	2/1/0/0	0
Protein mutations:	W456F (1679G>T 1680G>T) S461A (1693T>G 1695A>T) L462P (1696T>C 1697T>C 1698G>T) D465T (1705G>A 1706A>C 1707T>A) I467L (1711A>T 1713C>G) T473F (1729A>T 1730C>T 1731A>T) T475S (1735A>T 1737T>A) I476L (1738A>C) Q477T (1741C>A 1742A>C 1743G>A) R481K (1753C>A 1754G>A 1755T>A) A482Q (1756G>C 1757C>A 1758T>A) L484A (1762C>G 1763T>C 1764G>T) A486F (1768G>T 1769C>T) S487T (1771T>A 1773T>G) V490F (1780G>T 1782T>C) V491M (1783G>A 1785T>G) M494V (1792A>G 1794G>T) Y496M (1798T>A 1799A>T 1800T>G) M500L (1810A>T 1812G>A) R501K (1814G>A) Q503E (1819C>G) K504S (1823A>G 1824G>C) Y505del (1825_1827delTAT) S506P (1828T>C) T507L (1831A>C 1832C>T 1833C>T) F508Y (1835T>A) V509C (1837G>T 1838T>G 1839A>T) K510M (1841A>T) Y513M (1849T>A 1850A>T 1851T>G) G514T (1852G>A 1853G>C) G515K (1855G>A 1856G>A) G515_G516insK (1857_1858insAAA) K517N (1863A>T) G518R (1864G>A) G519A (1868G>C) Q520V (1870C>G 1871A>T 1872A>G) G521R (1873G>A) A522V (1877C>T) E523D (1881A>T) P525E (1885C>G 1886C>A) P525_V526insN (1887_1888insAAT) V526A (1889T>C 1890T>C) K532Q (1906A>C 1908G>A) T533Q (1909A>C 1910C>A 1911A>G) I536F (1918A>T 1920C>T) R537S (1923A>T) K538R (1925A>G) D539Q (1927G>C 1929C>A) K541P (1933A>C 1934A>C 1935G>C)
Codon mutations:	TTG454TTA (1674G>A) GCG455GCC (1677G>C) TGG456TTT (1679G>T 1680G>T) GCA459GCT (1689A>T) TCA461GCT (1693T>G 1695A>T) TTG462CCT (1696T>C 1697T>C 1698G>T) TGT463TGC (1701T>C) CAG464CAA (1704G>A) GAT465ACA (1705G>A 1706A>C 1707T>A) CTC466CTG (1710C>G) ATC467TTG (1711A>T 1713C>G) CGC468CGA (1716C>A) ATA470ATT (1722A>T) CGT471CGA (1725T>A) AAA472AAG (1728A>G) ACA473TTT (1729A>T 1730C>T 1731A>T) GGA474GGG (1734A>G) ACT475TCA (1735A>T 1737T>A) ATA476CTA (1738A>C) CAG477ACA (1741C>A 1742A>C 1743G>A) GAT478GAC (1746T>C) TAT479TAC (1749T>C) CGT481AAA (1753C>A 1754G>A 1755T>A) GCT482CAA (1756G>C 1757C>A 1758T>A) CTG484GCT (1762C>G 1763T>C 1764G>T) GCT486TTT (1768G>T 1769C>T) TCT487ACG (1771T>A 1773T>G) CCC488CCA (1776C>A) GCA489GCC (1779A>C) GTT490TTC (1780G>T 1782T>C) GTT491ATG (1783G>A 1785T>G) CAG492CAA (1788G>A) GGT493GGA (1791T>A) ATG494GTT (1792A>G 1794G>T) GCA495GCC (1797A>C) TAT496ATG (1798T>A 1799A>T 1800T>G) GCA498GCC (1806A>C) ATG500TTA (1810A>T 1812G>A) AGA501AAA (1814G>A) GGA502GGG (1818A>G) CAA503GAA (1819C>G) AAG504AGC (1823A>G 1824G>C) TAT505del (1825_1827delTAT) TCT506CCT (1828T>C) ACC507CTT (1831A>C 1832C>T 1833C>T) TTT508TAT (1835T>A) GTA509TGT (1837G>T 1838T>G 1839A>T) AAG510ATG (1841A>T) ACA512ACT (1848A>T) TAT513ATG (1849T>A 1850A>T 1851T>G) GGT514ACT (1852G>A 1853G>C) GGG515AAG (1855G>A 1856G>A) GGG515_GGA516insAAA (1857_1858insAAA) AAA517AAT (1863A>T) GGA518AGA (1864G>A) GGT519GCT (1868G>C) CAA520GTG (1870C>G 1871A>T 1872A>G) GGA521AGA (1873G>A) GCA522GTA (1877C>T) GAA523GAT (1881A>T) GGG524GGT (1884G>T) CCA525GAA (1885C>G 1886C>A) CCA525_GTT526insAAT (1887_1888insAAT) GTT526GCC (1889T>C 1890T>C) TGT527TGC (1893T>C) TCC529TCT (1899C>T) GGT531GGA (1905T>A) AAG532CAA (1906A>C 1908G>A) ACA533CAG (1909A>C 1910C>A 1911A>G) ATC536TTT (1918A>T 1920C>T) AGA537AGT (1923A>T) AAA538AGA (1925A>G) GAC539CAA (1927G>C 1929C>A) TGT540TGC (1932T>C) AAG541CCC (1933A>C 1934A>C 1935G>C)
p27 CA (NP_955569.1)	202	244	17.6%	196	63.4%	43 (100%)	25 (58.1%)	0/0/0/0	0
Protein mutations:	W204F (1679G>T 1680G>T) S209A (1693T>G 1695A>T) L210P (1696T>C 1697T>C 1698G>T) D213T (1705G>A 1706A>C 1707T>A) I215L (1711A>T 1713C>G) T221F (1729A>T 1730C>T 1731A>T) T223S (1735A>T 1737T>A) I224L (1738A>C) Q225T (1741C>A 1742A>C 1743G>A) R229K (1753C>A 1754G>A 1755T>A) A230Q (1756G>C 1757C>A 1758T>A) L232A (1762C>G 1763T>C 1764G>T) A234F (1768G>T 1769C>T) S235T (1771T>A 1773T>G) V238F (1780G>T 1782T>C) V239M (1783G>A 1785T>G) M242V (1792A>G 1794G>T) Y244M (1798T>A 1799A>T 1800T>G)
Codon mutations:	TTG202TTA (1674G>A) GCG203GCC (1677G>C) TGG204TTT (1679G>T 1680G>T) GCA207GCT (1689A>T) TCA209GCT (1693T>G 1695A>T) TTG210CCT (1696T>C 1697T>C 1698G>T) TGT211TGC (1701T>C) CAG212CAA (1704G>A) GAT213ACA (1705G>A 1706A>C 1707T>A) CTC214CTG (1710C>G) ATC215TTG (1711A>T 1713C>G) CGC216CGA (1716C>A) ATA218ATT (1722A>T) CGT219CGA (1725T>A) AAA220AAG (1728A>G) ACA221TTT (1729A>T 1730C>T 1731A>T) GGA222GGG (1734A>G) ACT223TCA (1735A>T 1737T>A) ATA224CTA (1738A>C) CAG225ACA (1741C>A 1742A>C 1743G>A) GAT226GAC (1746T>C) TAT227TAC (1749T>C) CGT229AAA (1753C>A 1754G>A 1755T>A) GCT230CAA (1756G>C 1757C>A 1758T>A) CTG232GCT (1762C>G 1763T>C 1764G>T) GCT234TTT (1768G>T 1769C>T) TCT235ACG (1771T>A 1773T>G) CCC236CCA (1776C>A) GCA237GCC (1779A>C) GTT238TTC (1780G>T 1782T>C) GTT239ATG (1783G>A 1785T>G) CAG240CAA (1788G>A) GGT241GGA (1791T>A) ATG242GTT (1792A>G 1794G>T) GCA243GCC (1797A>C) TAT244ATG (1798T>A 1799A>T 1800T>G)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43