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 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 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