Genome Detective

NGS Details (SRR3458562_Metagenome_example): Mason-Pfizer monkey virus

Assembly

Coverage Length

575 (2 contig(s))

Depth Of Coverage

1.2

Number Of Reads

Reads Per Million

0.32 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

Mason-Pfizer monkey virus (Taxonomy ID: 11855)

Reference Genome

NC_001550.1

NT Identity (%)

80.212

AA Identity (%)

83.5689

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

666.0 (NT) + 3600.0 (AA) = 4266.0

Concordance (%)

79.2201

Alignment Method

Global, seeded, nucleotide + amino acids (AGA)

NT Alignment

Download alignment (FASTA)

Region Bam File

Download BAM file (.bam)

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 1312 and ends at position 2140 relative to NC_001550.1 reference sequence.

NC_001550.1

SRR3458562_Metagenome_example-NC_001550.1-71-0

NC_001550.1

SRR3458562_Metagenome_example-NC_001550.1-71-0

NC_001550.1

SRR3458562_Metagenome_example-NC_001550.1-71-0

GCCACCATTAAATGAGACTTGATCAGAACACTGTCTTGTCTCCATTTCTTGTGTCTCTTGTTCCCTTCAATTCCCACTCCCTCCTCCAGGTTCCTACTGTTGATCCCGCGGGTCGGGACAGTTGGCGCCCAACGTGGGGCTGGATACGAGGGAATTTCGTGAGGAAGACGACGCGTTCGCCGGCCGGCGATTAAAAGTGAAAGTAAACTCTCTTGGCCGCCGCGGGAACCTGCCGCGTTGGACCTGAAAGTAAGTGTTGCGCTCGGATATGGGGCAAGAATTAAGCCAGCATGAACGTTATGTAGAACAATTGAAGCAGGCTTTAAAGACACGGGGAGTAAAGGTTAAATATGCTGATCTTTTGAAATTTTTTGATTTTGTGAAGGATACTTGTCCTTGGTTTCCGCAAGAGGGAACCATAGATATTAAACGGTGGCGTAGAGTAGGCGACTGTTTCCAAGACTATTACAATACTTTTGGCCCGGAGAAAGTCCCAGTAACTGCATTCTCTTACTGGAACTTAATTAAAGAATTGATAGATAAGAAAGAAGTTAACCCACAAGTAATGGCTGCCGTAGCCCAAACTGAAGAAATTTTAAAAAGTAATTCTCAAACAGACCTCACAAAGACCTCTCAAAACCCAGACTTGGACCTTATTTCCCTTGATAGCGACGATGAAGGAGCTAAAAGTTCCTCTCTACAAGATAAAGGTTTATCAAGTACTAAAAAACCAAAAAGATTCCCAGTTCTGTTAACAGCACAAACTAGTAAAGACCCTGAAGACCCCAACCCCTCAGAGGTAGACTGGGACGGCTTGGAAGATGAGGCAGCGAAATATCATAATCCCGATTGGCCTCCCTTCCTAACCCGTCCACCTCCTTACAATAAAGCTACTCCTTCCGCACCCACTGTAATGGCGGTTGTTAATCCAAAAGAGGAGCTCAAAGAAAAAATTGCTCAATTAGAGGAACAGATTAAATTAGAAGAGTTACACCAGGCA

CTAATTTCCAAATTACAAAAACTAAAAACAGGGAATGAAACTGTAACTCACCCAGACACAGCAGGAGGCCTTTCTCGCACGCCTCACTGGCCAGGGCAACATATCCCTAAAGGAAAATGTTGCGCCAGTCGAGAAAAGGAAGAACAAATCCCAAAAGATATTTTCCCAGTGACTGAAACCGTTGATGGGCAAGGTCAAGCCTGGAGACACCATAATGGTTTTGATTTTGCCGTCATAAAAGAATTAAAAACAGCTGCTTCCCAATATGGGGCTACTGCCCCATACACATTAGCCATAGTGGAATCTGTAGCGGACAATTGGCTTACCCCTACAGATTGGAATACGCTTGTTAGGGCAGTCCTCTCAGGAGGAGATCACTTACTGTGGAAATCTGAGTTTTTTGAAAATTGCAGAGATACGGCTAAAAGAAACCAACAAGCCGGTAATGGCTGGGATTTTGACATGTTAACAGGTTCGGGTAATTATTCCAGCACCGATGCACAAATGCAGTATGATCCAGGATTGTTTGCTCAAATTCAAGCGGCTGCTACAAAAGCCTGGAGAAAACTTCCCGTTAAGGGAGACCCAGGAGCCTCCCTTACAGGAGTCAAACAAGGACCCGATGAGCCATTTGCAGATTTCGTACACAGACTTATAACAACTGCTGGGAGAATCTTTGGAAGTGCTGAGGCCGGTGTAGACTATGTAAAACAACTAGCATATGAAAATGCTAATCCAGCTTGTCAGGCAGCCATTCGCCCCTATAGAAAGAAGACAGATTTAACTGGCTATATCCGTCTTTGCTCGGATATTGGGCCCTCTTATCAGCAAGGCCTGGCCATGGCCGCCGCCTTTAGCGGGCAGACTGTAAAAGATTTTCTTAACAACAAAAATAAAGAGAAAGGAGGGTGTTGCTTTAAATGCGGTAAAAAAGGACACTTTGCAAAAAATTGTCATGAACATGCACATAACAATGCTGAACCAAAAGTTCCCGGACTCT

GCCCTAGATGTAAAAGAGGGAAACATTGGGCCAATGAATGCAAATCCAAAACTGATAATCAAGGAAACCCAATACCACCCCATCAGGGAAACGGGTGGAGGGGCCAGCCCCAGGCCCCGAAACAAGCTTATGGGGCAGTCAGCTTTGTTCCAGCCAACAAAAACAACCCATTTCAAAGCTTACCAGAGCCACCCCAGGAAGTGCAGGATTGGACCTCTGTTCCACCTCCCACACAGTATTAACGCCTGAAATGGGGCCCCAAGCGTTAAGCACTGGAATATATGGACCACTGCCTCCCAACACTTTTGGATTAATCCTAGGCCGAAGTAGCATTACTATGAAGGGTCTACAAGTTTATCCAGGAGTAATTGATAATGACTATACCGGAGAAATTAAAATTATGGCAAAAGCTGTTAACAATATTGTTACTGTCTCTCAAGGCAACAGAATAGCTCAATTAATCCTCCTGCCTCTGATCGAGACAGACAATAAGGTACAACAACCTTATAGAGGACAAGGAAGTTTTGGATCCTCAGACATATATTGGGTCCAACCTATTACTTGTCAAAAACCTTCCTTAACATTATGGTTAGATGACAAAATGTTCACAGGCTTAATAGATACGGGGGCTGATGTCACAATTATCAAGCTGGAGGACTGGCCTCCTAATTGGCCTATAACAGATACCTTAACCAATTTAAGAGGAATAGGACAAAGTAACAACCCTAAACAAAGTTCTAAATATCTTACTTGGAGAGATAAAGAAAACAATTCTGGTCTCATCAAACCGTTTGTTATTCCTAACTTACCTGTCAATCTTTGGGGCCGAGATTTACTTTCTCAAATGAAAATTATGATGTGTAGCCCCAATGACATAGTAACTGCTCAAATGTTAGCCCAGGGCTACAGCCCAGGAAAAGGGTTAGGAAAAAAGGAAAATGGCATTCTACATCCTATCCCAAATCAAGGACAATCTAACAAAAAAGGTTTTGGAAATTTT

TAACTGCGGCCATTGACATACTTGCACCCCAACAGTGCGCTGAACCCATCACGTGGAAATCAGACGAACCTGTCTGGGTTGATCAGTGGCCATTAACCAATGACAAACTTGCTGCTGCCCAACAGTTAGTGCAAGAACAGTTAGAGGCAGGACATATTACTGAAAGTAGTTCTCCCTGGAACACTCCCATATTTGTTATAAAAAAGAAATCTGGTAAATGGAGGCTCTTACAAGATTTACGAGCCGTTAATGCCACTATGGTATTAATGGGAGCTTTACAACCTGGATTACCCTCCCCGGTGGCTATCCCACAAGGGTATCTTAAAATAATTATTGATCTCAAGGATTGTTTCTTTTCTATTCCCCTTCATCCTAGTGACCAAAAAAGATTTGCCTTCAGCCTACCATCCACAAATTTTAAAGAACCTATGCAACGTTTTCAGTGGAAGGTTTTACCACAAGGTATGGCCAACAGTCCTACCTTATGTCAAAAATATGTGGCCACAGCCATACATAAGGTTAGACATGCCTGGAAACAAATGTATATTATACATTACATGGATGACATCCTAATAGCTGGTAAAGATGGACAACAAGTTTTGCAATGCTTTGATCAACTCAAACAAGAGTTGACTGCAGCTGGGTTACATATAGCCCCAGAAAAAGTTCAATTACAAGATCCCTACACATATTTAGGATTTGAACTTAATGGTCCTAAAATCACTAATCAAAAAGCAGTCATTCGTAAAGATAAATTACAGACTCTTAATGATTTCCAAAAACTTTTAGGAGACATCAATTGGCTCAGACCATATCTAAAACTCACTACTGGAGACTTAAAACCCTTATTCGACACCCTTAAAGGAGACTCTGACCCCAATTCCCATAGATCCTTATCAAAAGAAGCTCTTGCCTCACTTGAAAAGGTAGAGACAGCCATTGCAGAACAATTCGTTACTCACATAAATTATTCACTACCATTAATTTTCCTCATATTCAA

CACAGCCCTGACACCTACTGGTTTGTTTTGGCAAGACAATCCTATTATGTGGATCCACCTGCCTGCATCCCCTAAAAAGGTGTTACTTCCCTACTACGACGCTATAGCAGATTTAATCATACTAGGGAGAGACCATAGTAAAAAATATTTTGGAATTGAACCCTCTACAATCATACAACCATATTCTAAGTCTCAGATTGATTGGTTAATGCAAAACACTGAAATGTGGCCAATTGCCTGTGCCTCCTTTGTTGGCATCCTAGATAACCATTATCCACCAAATAAACTTATCCAGTTCTGTAAACTACATACCTTTGTTTTCCCTCAAATCATTAGTAAAACACCCTTAAACAATGCCTTATTAGTTTTTACTGATGGCTCTTCCACTGGGATGGCCGCATATACTCTTACTGATACCACCATCAAATTCCAAACTAATCTTAATTCGGCTCAACTAGTAGAACTACAAGCTTTAATTGCAGTCTTATCAGCCTTCCCTAATCAACCTCTTAATATTTACACTGACAGTGCTTACTTAGCCCACTCAATACCCCTACTTGAAACTGTCGCACAAATTAAACACATATCAGAAACAGCTAAACTGTTCCTACAGTGCCAGCAACTCATATACAATAGATCCATACCTTTTTATATTGGACATGTCAGGGCCCATTCTGGACTACCTGGACCCATAGCTCAAGGCAACCAACGAGCTGACTTGGCAACTAAAATCGTGGCTAGTAACATAAACACAAACCTCGAATCAGCTCAAAATGCTCATACCTTACATCACCTCAATGCCCAGACTTTAAGACTTATGTTTAACATTCCTAGAGAACAAGCTAGACAAATTGTTAAGCAATGTCCTATATGTGTAACTTATCTACCAGTCCCTCATTTAGGAGTTAATCCTAGGGGATTATTTCCCAACATGATTTGGCAAATGGATGTTACACACTACTCAGAATTTGGCAATTTAAAATATATTCATGTATCTATA

GATACATTCAGTGGATTCCTACTGGCCACTCTACAAACAGGAGAAACTACAAAACATGTCATAACCCATTTACTCCATTGCTTCTCTATTATTGGACTCCCTAAACAAATTAAAACGGATAACGGTCCTGGATACACCTCTAAAAATTTTCAAGAATTTTGCTCCACACTTCAAATTAAACATATTACTGGAATCCCCTATAACCCCCAAGGCCAAGGAATAGTTGAAAGAGCCCACTTATCTCTTAAAACCACCATTGAAAAGATAAAAAAGGGGGAATGGTACCCTAGGAAGGGTACCCCCAGGAACATCCTCAATCATGCACTCTTTATTCTAAATTTTTTAAATTTAGATGATCAAAATAAATCAGCAGCTGATCGTTTTTGGCATAATAACCCCAAAAAACAATTTGCCATGGTAAAATGGAAAGATCCATTAGATAATACATGGCATGGCCCCGATCCAGTGTTAATTTGGGGCAGAGGTTCAGTCTGTGTTTACTCTCAAACCTATGATGCCGCTAGATGGCTACCAGAACGGTTAGTAAGACAGGTGTCTAACAATAACCAATCCAGGGAGTGATTCTCTCCCTGAGATCGCTCTTTCCCTTGTTCACAGATATGAACTTCAATTATCATTTCATCTGGAGCTTAGTGATACTATCTCAAATATCTCAAGTTCAAGCCGGTTTTGGAGATCCGCGTGAAGCCCTGGCAGAAATACAACAAAAACATGGTAAACCTTGTGACTGTGCTGGAGGATATGTTTCCTCCCCACCGATTAACTCTCTTACAACTGTTTCTTGCTCTACTCATACTGCTTATTCAGTGACAAACTCCCTAAAATGGCAGTGTGTGTCAACTCCCACTACCCCTAGCAATACACATATAGGAAGTTGTCCCGGTGAATGCAACACGATCTCATATGATTCTGTACATGCCTCTTGCTATAACCACTATCAACAATGTAACATTGGTAATAAAACATATCTCACTGCCAC

TATAACTGGAGATAGAACTCCTGCCATTGGTGACGGGAATGTCCCTACAGTACTAGGGACTAGTCACAACCTCATTACAGCAGGCTGTCCCAATGGTAAAAAGGGCCAAGTGGTCTGTTGGAATAGCCGACCTTCTGTTCATATATCTGATGGAGGAGGGCCTCAAGATAAGGCCCGCGACATTATAGTAAATAAAAAGTTTGAGGAATTGCACAGGTCGCTGTTCCCAGAACTTTCTTACCATCCTCTGGCCTTGCCCGAAGCCCGTGGTAAAGAAAAAATTGACGCACACACTCTTGATCTCCTTGCCACTGTACATAGTTTACTCAATGCTTCCCAACCCAGTTTAGCCGAAGATTGCTGGCTGTGCTTACAGTCAGGAGATCCCGTTCCTCTTGCCCTGCCCTATAATGATACACTCTGCTCTAACTTTGCCTGTTTATCTAATCACTCCTGCCCTTTAACCCCCCCTTTTTTAGTACAGCCCTTTAACTTCACTGATTCCAATTGCCTTTACGCTCATTATCAAAACAACTCATTTGACATAGATGTAGGTCTAGCTAGCTTTACTAATTGCTCTAGCTATTATAACGTTTCTACAGCCTCCAAACCCTCTAATTCCCTATGCGCCCCAAACAGCTCGGTTTTTGTATGCGGTAACAATAAGGCATACACTTATCTACCCACAAATTGGACGGGAAGTTGTGTACTTGCTACTCTTTTGCCCGATATAGACATCATTCCAGGTAGTGAGCCTGTCCCCATTCCAGCTATTGATCATTTTTTAGGCAAAGCCAAAAGAGCAATCCAACTTATCCCCCTGTTCGTAGGGTTAGGTATAACTACTGCAGTATCTACTGGGGCTGCTGGTCTAGGGGTTTCCATCACTCAATATACAAAATTATCTCATCAACTAATATCAGATGTTCAAGCTATTTCTAGCACTATACAAGATCTCCAAGATCAGGTAGACTCTCTAGCAGAAGTAGTACTGCAAAAC

AGAAGAGGATTAGATCTACTTACAGCAGAGCAGGGAGGTATCTGCTTAGCCTTACAGGAAAAATGTTGTTTCTACGCCAATAAATCTGGAATCGTCAGAGACAAGATTAAAAACCTACAAGACGACTTAGAAAGACGCCGAAGACAACTGATCGACAACCCATTTTGGACCAGTTTTCATGGATTCCTCCCTTATGTTATGCCCCTATTAGGCCCTTTGCTTTGCTTATTGCTTGTGTTATCTTTCGGTCCAATTATTTTCAACAAGCTTATGACCTTTATTAAACATCAAATTGAGAGCATCCAGGCCAAACCTATACAAGTCCATTATCATCGCCTTGAACAAGAAGACAGTGGTGGCTCATATTTGACCTTAACATAGGCCACCTCCCCTGTGAGCTAGACTGGACAGCCAATGACGGGTAAGAGAGTGACATTTCTCACTAACCTAAGACAGGAGGGCCGTCAAAGCTACTGCCTAATCCAATGACGGGTAATAGTGACAAGAAATGTATCACTCCAACCTAAGACAGGCGCAGCCTCCGAGGGATGTGTCTTTTGTTTTTTATAATTAAAAAGGGTGACATGTCCGGAGCCGTGCTGCCCGGATGATGTCTTGGCCTCTGTTTGCTCTAGCTCCATGTTATGAATTTAAGATGGCGTATTTCCTGGTTCTTCTCCGTCTTACTTTCCCGCCGGCGCGAATGTTTCCCGCTCTTGGGCTTACGTGGCTTTCCTTGCTCTGCTACTGAGCATGCGCCCAGTATCTTTCCCCTCCCACTTGCTGCCTGTGTATATAAGGCAACACATTGCCACCATTAAATGAGACTTGATCAGAACACTGTCTTGTCTCCATTTCTTGTGTCTCTTGTTCCCTTCAATTCCCACTCCCTCCTCCAGGTTCCTACTGTTGATCCCGCGGGTCGGGACAGTTTTCGTTTTCTGTCCGGAGCCGTGCTGCCCGGATGATGTCTTGGCCTCTGTTTGCTCTAGCTCCATGT

TATGAATTTAAGATGGCGTATTTCCTGGTTCTTCTCCGTCTTACTTTCCCGCCGGCGCGAATGTTTCCCGCTCTTGGGCTTACGTGGCTTTCCTTGCTCTGCTACTGAGCATGCGCCCAGTATCTTTCCCCTCCCACTTGCTGCCTGTGTATATAAGGCAACACATTGCCACCATTAAATGAGACTTGATCAGAACACTGTCTTGTCTCCATTTCTTGTGTCTCTTGTTCCCTTCAATTCCCACTCCCTCCTCCAGGTTCCTACTGTTGATCCCGCGGGTCGGGACAGTTGGCGCCCAACGTGGGGCACGAACCCACGACCCTGGGATTAAGAGTCCCATGCTCTACCGACTGGATGATGTCTTGGCCTCTGTTTGCTCTAGCTCCATGTTATGAATTTAAGATGGCGTATTTCCTGGTTCTTCTCCGTCTTACTTTCCCGCCGGCGCGAATGTTTCCCGCTCTTGGGCTTACGTGGCTTTCCTTGCTCTGCTACTGAGCATGCGCCCAGTATCTTTCCCCTCCCACTTGCTGCCTGTGTATATAAGGCAACACATT

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

.......................................................................................................................................................................................................................................................................................................................GGAGAATTGGCTCACTCCTACAGACTGGAATACCTTAGTTAGGGCAGTCCTTTCTGGGGGAGACCATTTAATTTGGAAGTCAGAGTTATTTGAAAATTGTAGAGACACGGATAAAAGAAATCAACAGGCAGGATAG---------TTTGATATGTTAACCGGTTCAGGTAACTATGCAGACACTCAGGCCCAAATGCTATATGATCCTGGCTTGTTTTCACAAATCCAGGCAGCTGCTACGAAAGCCTGGAGGAAACTCCCAGTTAAAGGAGACCCAGGGGCCTCACTCACGGCAGTCAAACAAGGAACGGATGAGCCGTTCTCAGATTTTGTACACAGACTCATGACTACGGCAGGTAGAATTTTTGGAAATGCAGAAACGGGTGTA..............................................................................................................................................................................................................................................................TCATGAAAACCAAAATAAAAATCCAGAAGCAAAAATTCCAGGCCTTT

GCCCAAGATGTAAAAGAGGAAGGCACTGGGCAAACGAATGTAAATCTAAAACTGACAGTCAAGGAAATCCTTTATCCCCTAGGCAGGGAAACGGGATGAGGGGCCAGCCTCAGGCCCCGAAACAAGCATATGGGGCAGTC............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

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gag

MGQELSQHERYVEQLKQALKTRGVKVKYADLLKFFDFVKDTCPWFPQEGTIDIKRWRRVGDCFQDYYNTFGPEKVPVTAFSYWNLIKELIDKKEVNPQVMAAVAQTEEILKSNSQTDLTKTSQNPDLDLISLDSDDEGAKSSSLQDKGLSSTKKPKRFPVLLTAQTSKDPEDPNPSEVDWDGLEDEAAKYHNPDWPPFLTRPPPYNKATPSAPTVMAVVNPKEELKEKIAQLEEQIKLEELHQALISKLQKLKTGNETVTHPDTAGGLSRTPHWPGQHIPKGKCCASREKEEQIPKDIFPVTETVDGQGQAWRHHNGFDFAVIKELKTAASQYGATAPYTLAIVESVADNWLTPTDWNTLVRAVLSGGDHLLWKSEFFENCRDTAKRNQQAGNGWDFDMLTGSGNYSSTDAQMQYDPGLFAQIQAAATKAWRKLPVKGDPGASLTGVKQGPDEPFADFVHRLITTAGRIFGSAEAGVDYVKQLAYENANPACQAAIRPYRKKTDLTGYIRLCSDIGPSYQQGLAMAAAFSGQTVKDFLNNKNKEKGGCCFKCGKKGHFAKNCHEHAHNNAEPKVPGLCPRCKRGKHWANECKSKTDNQGNPIPPHQGN

GWRGQPQAPKQAYGAVSFVPANKNNPFQSLPEPPQEVQDWTSVPPPTQY*

GMRGQPQAPKQAYGAV..................................

gag-pro-pol-env_1

RVEGPAPGPETSLWGSQLCSSQQKQPISKLTRATPGSAGLDLCSTSHTVLTPEMGPQALSTGIYGPLPPNTFGLILGRSSITMKGLQVYPGVIDNDYTGEIKIMAKAVNNIVTVSQGNRIAQLILLPLIETDNKVQQPYRGQGSFGSSDIYWVQPITCQKPSLTLWLDDKMFTGLIDTGADVTIIKLEDWPPNWPITDTLTNLRGIGQSNNPKQSSKYLTWRDKENNSGLIKPFVIPNLPVNLWGRDLLSQMKIMMCSPNDIVTAQMLAQGYSPGKGLGKKENGILHPIPNQGQSNKKGFGNF

RDEGPASGPETSIWGSX..............................................................................................................................................................................................................................................................................................

gag-pro-pol

LTAAIDILAPQQCAEPITWKSDEPVWVDQWPLTNDKLAAAQQLVQEQLEAGHITESSSPWNTPIFVIKKKSGKWRLLQDLRAVNATMVLMGALQPGLPSPVAIPQGYLKIIIDLKDCFFSIPLHPSDQKRFAFSLPSTNFKEPMQRFQWKVLPQGMANSPTLCQKYVATAIHKVRHAWKQMYIIHYMDDILIAGKDGQQVLQCFDQLKQELTAAGLHIAPEKVQLQDPYTYLGFELNGPKITNQKAVIRKDKLQTLNDFQKLLGDINWLRPYLKLTTGDLKPLFDTLKGDSDPNSHRSLSKEALASLEKVETAIAEQFVTHINYSLPLIFLIFNTALTPTGLFWQDNPIMWIHLPASPKKVLLPYYDAIADLIILGRDHSKKYFGIEPSTIIQPYSKSQIDWLMQNTEMWPIACASFVGILDNHYPPNKLIQFCKLHTFVFPQIISKTPLNNALLVFTDGSSTGMAAYTLTDTTIKFQTNLNSAQLVELQALIAVLSAFPNQPLNIYTDSAYLAHSIPLLETVAQIKHISETAKLFLQCQQLIYNRSIPFYIGHVRAHSGLPGPIAQGNQRADLATKIVASNINTNLESAQNAHTLHHLNAQTLRLMFNIPREQARQIVKQCPICVTYLPVPHLGVNPRGLFPNMIWQMDVTHYSEFGNLKYIHVSIDTFSGFLLATLQTGETTKHVITHLLHCFSIIGLPKQIKTDNGPGYTSKNFQEFCSTLQIKHITGIPYNPQGQGIVERAHLSLKTTIEKIKKGEWYPRKGTPRNILNHALFILNFLNLDDQNKSAADRFWHNNPKKQFAMVKWKDPLDNTWHGPDPVLIWGRGSVCVYSQTYDAARWLPERLVRQVSNNNQSRE*

gag-pro-pol-env_2

MNFNYHFIWSLVILSQISQVQAGFGDPREALAEIQQKHGKPCDCAGGYVSSPPINSLTTVSCSTHTAYSVTNSLKWQCVSTPTTPSNTHIGSCPGECNTISYDSVHASCYNHYQQCNIGNKTYLTATITGDRTPAIGDGNVPTVLGTSHNLITAGCPNGKKGQVVCWNSRPSVHISDGGGPQDKARDIIVNKKFEELHRSLFPELSYHPLALPEARGKEKIDAHTLDLLATVHSLLNASQPSLAEDCWLCLQSGDPVPLALPYNDTLCSNFACLSNHSCPLTPPFLVQPFNFTDSNCLYAHYQNNSFDIDVGLASFTNCSSYYNVSTASKPSNSLCAPNSSVFVCGNNKAYTYLPTNWTGSCVLATLLPDIDIIPGSEPVPIPAIDHFLGKAKRAIQLIPLFVGLGITTAVSTGAAGLGVSITQYTKLSHQLISDVQAISSTIQDLQDQVDSLAEVVLQNRRGLDLLTAEQGGICLALQEKCCFYANKSGIVRDKIKNLQDDLERRRRQLIDNPFWTSFHGFLPYVMPLLGPLLCLLLVLSFGPIIFNKLMTFIKHQIESIQAKPIQVHYHRLEQEDSGGSYLTLT*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	1312	2140	6.7%	666	59.8%	566 (98.4%)	454 (79.0%)	0/9
Mutations:	1315C>G, 1324T>C, 1327C>T, 1336T>C, 1345G>C, 1346C>T, 1348T>A, 1363C>T, 1366A>T, 1369A>G, 1375T>C, 1378C>T, 1382C>A, 1384G>T, 1390A>G, 1393T>A, 1399T>A, 1411C>T, 1417T>C, 1422C>A, 1432C>T, 1438A>G, 1441C>A, 1444T>A, 1445A>T, 1447T>G, 1448_1456delGGCTGGGAT, 1462C>T, 1471A>C, 1477G>A, 1483T>C, 1487T>G, 1489C>A, 1490A>G, 1491G>A, 1495C>T, 1496G>C, 1498T>G, 1501A>C, 1509A>T, 1510G>A, 1519A>T, 1522A>C, 1529G>T, 1531T>A, 1537T>C, 1540A>G, 1543G>A, 1552A>G, 1564A>G, 1570T>C, 1573C>A, 1579G>A, 1591A>G, 1597C>A, 1600T>C, 1603A>G, 1605G>C, 1619C>A, 1621C>G, 1630A>G, 1633T>C, 1634G>T, 1642C>T, 1654T>C, 1657A>G, 1660A>T, 1663T>G, 1666T>A, 1669G>T, 1675C>T, 1683G>A, 1687T>A, 1690G>A, 1691G>A, 1693C>G, 1961C>A, 1963T>C, 1964G>C, 1965C>A, 1967C>A, 1972C>A, 1976G>C, 1978T>A, 1982C>G, 1988G>A, 1993C>A, 1996A>C, 1999C>T, 2005T>A, 2020G>A, 2022A>G, 2023A>G, 2026T>C, 2032C>A, 2035T>C, 2041C>T, 2047C>T, 2056T>C, 2058A>G, 2068C>T, 2071A>T, 2072A>T, 2075C>T, 2077A>C, 2080C>T, 2081C>A, 2082A>G, 2083T>G, 2096T>A, 2097G>T, 2110C>T, 2128T>A
CDS

gag-pro-pol	349	625	10.8%	1199	82.6%	189 (98.4%)	157 (81.8%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), V610D (2096T>A 2097G>T), P615S (2110C>T), L621I (2128T>A)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), GTG610GAT (2096T>A 2097G>T), CCA615TCA (2110C>T), TTA621ATA (2128T>A)
gag-pro-pol-env_1	349	625	21.1%	1199	82.6%	189 (98.4%)	157 (81.8%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), V610D (2096T>A 2097G>T), P615S (2110C>T), L621I (2128T>A)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), GTG610GAT (2096T>A 2097G>T), CCA615TCA (2110C>T), TTA621ATA (2128T>A)
gag	349	624	29.0%	1202	83.0%	188 (98.4%)	159 (83.2%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), W610M (2096T>A 2097G>T)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), TGG610ATG (2096T>A 2097G>T), CCC614CCT (2110C>T), GCT620GCA (2128T>A)
Proteins

RT-IN (NP_056891.1)	349	625	10.8%	1199	82.6%	189 (98.4%)	157 (81.8%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), V610D (2096T>A 2097G>T), P615S (2110C>T), L621I (2128T>A)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), GTG610GAT (2096T>A 2097G>T), CCA615TCA (2110C>T), TTA621ATA (2128T>A)
RT-IN (NP_954565.2)	349	625	10.8%	1199	82.6%	189 (98.4%)	157 (81.8%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), V610D (2096T>A 2097G>T), P615S (2110C>T), L621I (2128T>A)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), GTG610GAT (2096T>A 2097G>T), CCA615TCA (2110C>T), TTA621ATA (2128T>A)
DU (NP_954564.1)	38	100	26.9%	403	73.3%	63 (100%)	47 (74.6%)	0/0/0/0	0
Protein mutations:	H40N (1961C>A 1963T>C), A41Q (1964G>C 1965C>A), H42N (1967C>A), N43K (1972C>A), A45P (1976G>C 1978T>A), P47A (1982C>G), V49I (1988G>A), K60R (2022A>G 2023A>G), N72S (2058A>G), I77L (2072A>T), P78S (2075C>T 2077A>C), H80R (2081C>A 2082A>G 2083T>G), V85D (2096T>A 2097G>T), P90S (2110C>T), L96I (2128T>A)
Codon mutations:	CAT40AAC (1961C>A 1963T>C), GCA41CAA (1964G>C 1965C>A), CAT42AAT (1967C>A), AAC43AAA (1972C>A), GCT45CCA (1976G>C 1978T>A), CCA47GCA (1982C>G), GTT49ATT (1988G>A), CCC50CCA (1993C>A), GGA51GGC (1996A>C), CTC52CTT (1999C>T), CCT54CCA (2005T>A), GGG59GGA (2020G>A), AAA60AGG (2022A>G 2023A>G), CAT61CAC (2026T>C), GCC63GCA (2032C>A), AAT64AAC (2035T>C), TGC66TGT (2041C>T), TCC68TCT (2047C>T), GAT71GAC (2056T>C), AAT72AGT (2058A>G), AAC75AAT (2068C>T), CCA76CCT (2071A>T), ATA77TTA (2072A>T), CCA78TCC (2075C>T 2077A>C), CCC79CCT (2080C>T), CAT80AGG (2081C>A 2082A>G 2083T>G), GTG85GAT (2096T>A 2097G>T), CCA90TCA (2110C>T), TTA96ATA (2128T>A)
Pr95 (NP_056892.1)	349	625	21.1%	1199	82.6%	189 (98.4%)	157 (81.8%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), V610D (2096T>A 2097G>T), P615S (2110C>T), L621I (2128T>A)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), GTG610GAT (2096T>A 2097G>T), CCA615TCA (2110C>T), TTA621ATA (2128T>A)
Pr78 (NP_056893.1)	349	624	29.0%	1202	83.0%	188 (98.4%)	159 (83.2%)	0/3/0/0	1
Protein mutations:	D349E (1315C>G), L372I (1382C>A 1384G>T), F377L (1399T>A), A385D (1422C>A), N393* (1445A>T 1447T>G), G394_D396del (1448_1456delGGCTGGGAT), S407A (1487T>G 1489C>A), S408D (1490A>G 1491G>A), D410Q (1496G>C 1498T>G), Q414L (1509A>T 1510G>A), A421S (1529G>T 1531T>A), G446A (1605G>C), P451T (1619C>A 1621C>G), A456S (1634G>T), I463M (1657A>G), S472N (1683G>A), A475T (1691G>A 1693C>G), H565N (1961C>A 1963T>C), A566Q (1964G>C 1965C>A), H567N (1967C>A), N568K (1972C>A), A570P (1976G>C 1978T>A), P572A (1982C>G), V574I (1988G>A), K585R (2022A>G 2023A>G), N597S (2058A>G), I602L (2072A>T), P603S (2075C>T 2077A>C), H605R (2081C>A 2082A>G 2083T>G), W610M (2096T>A 2097G>T)
Codon mutations:	GAC349GAG (1315C>G), CTT352CTC (1324T>C), ACC353ACT (1327C>T), GAT356GAC (1336T>C), ACG359ACC (1345G>C), CTT360TTA (1346C>T 1348T>A), CTC365CTT (1363C>T), TCA366TCT (1366A>T), GGA367GGG (1369A>G), GAT369GAC (1375T>C), CAC370CAT (1378C>T), CTG372ATT (1382C>A 1384G>T), AAA374AAG (1390A>G), TCT375TCA (1393T>A), TTT377TTA (1399T>A), TGC381TGT (1411C>T), GAT383GAC (1417T>C), GCT385GAT (1422C>A), AAC388AAT (1432C>T), CAA390CAG (1438A>G), GCC391GCA (1441C>A), GGT392GGA (1444T>A), AAT393TAG (1445A>T 1447T>G), GGC394_GAT396del (1448_1456delGGCTGGGAT), GAC398GAT (1462C>T), ACA401ACC (1471A>C), TCG403TCA (1477G>A), AAT405AAC (1483T>C), TCC407GCA (1487T>G 1489C>A), AGC408GAC (1490A>G 1491G>A), ACC409ACT (1495C>T), GAT410CAG (1496G>C 1498T>G), GCA411GCC (1501A>C), CAG414CTA (1509A>T 1510G>A), CCA417CCT (1519A>T), GGA418GGC (1522A>C), GCT421TCA (1529G>T 1531T>A), ATT423ATC (1537T>C), CAA424CAG (1540A>G), GCG425GCA (1543G>A), ACA428ACG (1552A>G), AGA432AGG (1564A>G), CTT434CTC (1570T>C), CCC435CCA (1573C>A), AAG437AAA (1579G>A), GGA441GGG (1591A>G), TCC443TCA (1597C>A), CTT444CTC (1600T>C), ACA445ACG (1603A>G), GGA446GCA (1605G>C), CCC451ACG (1619C>A 1621C>G), CCA454CCG (1630A>G), TTT455TTC (1633T>C), GCA456TCA (1634G>T), TTC458TTT (1642C>T), CTT462CTC (1654T>C), ATA463ATG (1657A>G), ACA464ACT (1660A>T), ACT465ACG (1663T>G), GCT466GCA (1666T>A), GGG467GGT (1669G>T), ATC469ATT (1675C>T), AGT472AAT (1683G>A), GCT473GCA (1687T>A), GAG474GAA (1690G>A), GCC475ACG (1691G>A 1693C>G), CAT565AAC (1961C>A 1963T>C), GCA566CAA (1964G>C 1965C>A), CAT567AAT (1967C>A), AAC568AAA (1972C>A), GCT570CCA (1976G>C 1978T>A), CCA572GCA (1982C>G), GTT574ATT (1988G>A), CCC575CCA (1993C>A), GGA576GGC (1996A>C), CTC577CTT (1999C>T), CCT579CCA (2005T>A), GGG584GGA (2020G>A), AAA585AGG (2022A>G 2023A>G), CAT586CAC (2026T>C), GCC588GCA (2032C>A), AAT589AAC (2035T>C), TGC591TGT (2041C>T), TCC593TCT (2047C>T), GAT596GAC (2056T>C), AAT597AGT (2058A>G), AAC600AAT (2068C>T), CCA601CCT (2071A>T), ATA602TTA (2072A>T), CCA603TCC (2075C>T 2077A>C), CCC604CCT (2080C>T), CAT605AGG (2081C>A 2082A>G 2083T>G), TGG610ATG (2096T>A 2097G>T), CCC614CCT (2110C>T), GCT620GCA (2128T>A)
p27 (NP_954560.1)	50	178	56.6%	796	88.3%	126 (97.7%)	110 (85.3%)	0/3/0/0	1
Protein mutations:	D50E (1315C>G), L73I (1382C>A 1384G>T), F78L (1399T>A), A86D (1422C>A), N94* (1445A>T 1447T>G), G95_D97del (1448_1456delGGCTGGGAT), S108A (1487T>G 1489C>A), S109D (1490A>G 1491G>A), D111Q (1496G>C 1498T>G), Q115L (1509A>T 1510G>A), A122S (1529G>T 1531T>A), G147A (1605G>C), P152T (1619C>A 1621C>G), A157S (1634G>T), I164M (1657A>G), S173N (1683G>A), A176T (1691G>A 1693C>G)
Codon mutations:	GAC50GAG (1315C>G), CTT53CTC (1324T>C), ACC54ACT (1327C>T), GAT57GAC (1336T>C), ACG60ACC (1345G>C), CTT61TTA (1346C>T 1348T>A), CTC66CTT (1363C>T), TCA67TCT (1366A>T), GGA68GGG (1369A>G), GAT70GAC (1375T>C), CAC71CAT (1378C>T), CTG73ATT (1382C>A 1384G>T), AAA75AAG (1390A>G), TCT76TCA (1393T>A), TTT78TTA (1399T>A), TGC82TGT (1411C>T), GAT84GAC (1417T>C), GCT86GAT (1422C>A), AAC89AAT (1432C>T), CAA91CAG (1438A>G), GCC92GCA (1441C>A), GGT93GGA (1444T>A), AAT94TAG (1445A>T 1447T>G), GGC95_GAT97del (1448_1456delGGCTGGGAT), GAC99GAT (1462C>T), ACA102ACC (1471A>C), TCG104TCA (1477G>A), AAT106AAC (1483T>C), TCC108GCA (1487T>G 1489C>A), AGC109GAC (1490A>G 1491G>A), ACC110ACT (1495C>T), GAT111CAG (1496G>C 1498T>G), GCA112GCC (1501A>C), CAG115CTA (1509A>T 1510G>A), CCA118CCT (1519A>T), GGA119GGC (1522A>C), GCT122TCA (1529G>T 1531T>A), ATT124ATC (1537T>C), CAA125CAG (1540A>G), GCG126GCA (1543G>A), ACA129ACG (1552A>G), AGA133AGG (1564A>G), CTT135CTC (1570T>C), CCC136CCA (1573C>A), AAG138AAA (1579G>A), GGA142GGG (1591A>G), TCC144TCA (1597C>A), CTT145CTC (1600T>C), ACA146ACG (1603A>G), GGA147GCA (1605G>C), CCC152ACG (1619C>A 1621C>G), CCA155CCG (1630A>G), TTT156TTC (1633T>C), GCA157TCA (1634G>T), TTC159TTT (1642C>T), CTT163CTC (1654T>C), ATA164ATG (1657A>G), ACA165ACT (1660A>T), ACT166ACG (1663T>G), GCT167GCA (1666T>A), GGG168GGT (1669G>T), ATC170ATT (1675C>T), AGT173AAT (1683G>A), GCT174GCA (1687T>A), GAG175GAA (1690G>A), GCC176ACG (1691G>A 1693C>G)
p14 NC (NP_954556.1)	38	97	61.9%	397	73.8%	60 (100%)	47 (78.3%)	0/0/0/0	0
Protein mutations:	H40N (1961C>A 1963T>C), A41Q (1964G>C 1965C>A), H42N (1967C>A), N43K (1972C>A), A45P (1976G>C 1978T>A), P47A (1982C>G), V49I (1988G>A), K60R (2022A>G 2023A>G), N72S (2058A>G), I77L (2072A>T), P78S (2075C>T 2077A>C), H80R (2081C>A 2082A>G 2083T>G), W85M (2096T>A 2097G>T)
Codon mutations:	CAT40AAC (1961C>A 1963T>C), GCA41CAA (1964G>C 1965C>A), CAT42AAT (1967C>A), AAC43AAA (1972C>A), GCT45CCA (1976G>C 1978T>A), CCA47GCA (1982C>G), GTT49ATT (1988G>A), CCC50CCA (1993C>A), GGA51GGC (1996A>C), CTC52CTT (1999C>T), CCT54CCA (2005T>A), GGG59GGA (2020G>A), AAA60AGG (2022A>G 2023A>G), CAT61CAC (2026T>C), GCC63GCA (2032C>A), AAT64AAC (2035T>C), TGC66TGT (2041C>T), TCC68TCT (2047C>T), GAT71GAC (2056T>C), AAT72AGT (2058A>G), AAC75AAT (2068C>T), CCA76CCT (2071A>T), ATA77TTA (2072A>T), CCA78TCC (2075C>T 2077A>C), CCC79CCT (2080C>T), CAT80AGG (2081C>A 2082A>G 2083T>G), TGG85ATG (2096T>A 2097G>T), CCC89CCT (2110C>T), GCT95GCA (2128T>A)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43