Genome Detective

NGS Details (ERR138007_norovirus_amplicon_example): Simian immunodeficiency virus

Assembly

Coverage Length

137 (1 contig(s))

Depth Of Coverage

1.7

Number Of Reads

Reads Per Million

4.26 rpm (after QC)

Ambiguities

Assembly Method

de novo + reference guided assembly

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants (VCF)

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Minority Variants (VCF)

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SNP Variants Table (CSV)

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Annotated Variants Table (CSV)

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Assignment

Type

Simian immunodeficiency virus (Taxonomy ID: 11723)

Subtype

unassigned

Reference Genome

NC_001549.1

NT Identity (%)

78.1022

AA Identity (%)

84.4444

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

158.0 (NT) + 576.0 (AA) = 734.0

Concordance (%)

78.0851

Alignment Method

Global, seeded, nucleotide + amino acids (AGA)

NT Alignment (FASTA)

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Region BAM File (ZIP)

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CDS Alignment (FASTA)

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Consensus Sequence (FASTA)

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Consensus Sequence with Ambiguities (FASTA)

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Consensus Contigs (FASTA)

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Genome Region

Sequence starts at position 1459 and ends at position 1595 relative to NC_001549.1 reference sequence.

NC_001549.1

ERR138007_norovirus_amplicon_example-NC_001549.1-0-0

NC_001549.1

ERR138007_norovirus_amplicon_example-NC_001549.1-0-0

NC_001549.1

ERR138007_norovirus_amplicon_example-NC_001549.1-0-0

TGGATGGGATATATTACTCTGAAAGAAGAGAAAAGATCCTGAATTTGTATGCCTTGAACGAGTGGGGAATAATAGATGATTGGCAAGCTTACTCACCAGGCCCGGGGATAAGGTACCCGAGAGTCTTTGGCTTCTGCTTTAAGCTAGTCCCAGTGGACCTGCATGAGGAGGCACGCAACTGTGAGAGACACTGTCTGATGCATCCAGCACAGATGGGGGAAGATCCTGATGGAATAGATCATGGAGAAGTCTTGGTCTGGAAGTTTGACCCGAAGTTGGCGGTGGAGTACCGCCCGGACATGTTTAAGGACATGCACGAACATGCAAAGCGCTAGTGTCAGCACTTTGCGGTTGGGACTTTCCGCCAGGGACTTTCCACAGTGGGTGGATCGGAGGCGGTACAGGGGCGGTACTGGGAGTGGCTTTCCCCTCAGAGCTGCATAAAAGCAGATGCTCGCTGGCTTGTAACTCAGTCTCTTACTAGGAGACCAGCTAGAGCCTGGGTGTTCGCTGGTTAGCCTAACCCGGTTGGCCACCGGGGGTAAGGACTCCTTGGCTTCATATAGCTCAATAAACCTGCTCGCTTAGTCGCTATATTGGAGTCAAGTGCTCATTGCTGCGCCGAGCCTCTAGAGGTGAACCTCTCTTACTGGGTTCTCCTGTACCCAGGTGGGAGAAACTCCAGCAGTGGCGCCCGAACAGGGACTTGAGAAGAGGCATCGGCACCGACCGCTGAGTTGCTGAGCGTCGGAGAGGGACGACTCAGGTAGGGTGAGAGCCTACGAGTTTTTTGCTACCTAGTCAGCGAGAAAGGCTAGGCCGCGACAGGGGCGCGGGTCCCATTAGTGGCAACCAACCCAGTTGGACGAAGGGTTGGTAGGGGACGGGTCGGAGCAATGGGCGGGGGTCACTCAGCACTGTCAGGGAGAAGCCTCGACACGTTCGAGAAGATTAGGCTACGTCCGAACGGGAAAAAGAAGTACCAAATTAAACATTTAAT

ATGGGCAGGAAAAGAAATGGAACGATTTGGGTTACATGAGAAACTTTTAGAAACAAAAGAAGGCTGTCAAAAAATCATAGAAGTTTTAACCCCGTTGGAACCGACAGGCTCCGAGGGGCTAAAAGCTCTGTTTAATTTGTGCTGCGTCATTTGGTGCATTCACGCAGAACAGAAAGTGAAAGACACAGAGGAAGCTGTAGTAACAGTTAAGCAACACTACCATCTAGTGGACAAAAATGAGAAAGCAGCTAAAAAGAAAAATGAGACAACAGCGCCACCTGGTGGCGAATCAAGAAATTACCCAGTAGTAAATCAGAATAATGCCTGGGTACACCAGCCTTTGTCTCCGCGCACGTTAAATGCGTGGGTCAAATGCGTGGAGGAAAAAAGGTGGGGAGCAGAAGTAGTCCCCATGTTCCAAGCACTCTCAGAGGGATGTCTCTCCTATGATGTAAATCAGATGCTCAATGTAATAGGAGACCATCAGGGGGCATTACAAATTCTTAAGGAAGTCATTAATGAAGAAGCAGCAGAGTGGGACAGGACACACAGACCACCAGCTGGCCCGTTACCAGCAGGGCAGCTAAGAGACCCGACAGGGTCAGATATAGCAGGAACTACCAGCTCAATTCAGGAACAAATAGAGTGGACCTTCAATGCCAATCCAAGAATAGACGTAGGGGCACAATACAGAAAATGGGTTATTTTGGGCTTACAAAAGGTAGTGCAGATGTACAATCCCCAAAAGGTCCTAGACATTCGACAGGGACCTAAAGAACCCTTCCAGGACTATGTAGACAGATTCTATAAAGCCCTGAGAGCAGAACAAGCACCACAGGATGTTAAAAATTGGATGACACAAACTTTGCTTATCCAGAATGCCAATCCGGATTGTAAATTGATTCTGAAAGGATTGGGAATGAATCCAACCTTGGAGGAAATGCTAATAGCTTGCCAGGGAGTAGGAGGGCCACAACATAAGGCTAAGCTAATGGTAGAA

ATGATGAGTAATGGACAGAATATGGTCCAAGTGGGACCTCAGAAAAAGGGCCCCCGAGGGCCGCTAAAATGCTTTAATTGTGGCAAATTTGGACATATGCAAAGGGAATGCAAGGCACCAAGACAGATCAAATGCTTTAAGTGCGGCAAAATTGGCCATATGGCAAAAGACTGCAAGAATGGACAGGCAAATTTTTTAGGGTATGGCCATTGGGGAGGAGCGAAACCAAGAAATTTTGTGCAATACAGAGGAGACACAGTTGGTCTGGAACCAACAGCCCCCCCAATGGAAACAGCTTACGATCCAGCAAAGAAGCTCCTCCAGCAGTATGCAGAGAAGGGACAGCGCCTGAGAGAGGAGAGAGAACAGACAAGGAAACAGAAGGAGAAAGAAGTGGAGGATGTTTCCTTGAGCTCCCTCTTTGGAGGAGACCAATGAAACGAGTCATCATAGAAGGAACGCCAGTGCAAGCCTTGTTAGATACAGGAGCAGATGACACTATAATTCAAGAAAAGGACTTGCACTTTCCCCCACATAAACCATGGCGTTCCAAGGTAGTAGGAGGTATAGGAGGAGGGATTCATGTCAAAGAATATCAGGGGGTACAAGTACAATTGGAGGATAAAATCATCACCGGCTCAATTCTAATAGGAAGTACACCAATCAATATTATAGGAAGAAATATTTTAGCTCAGGCAGGCATGAAATTAGTTATGGGAGTTCTATCTAGTCAGATTGAGGAAACAAAAGTACAACTAAAAGAAGGGAAAGATGGACCTAAATTGAAACAATGGCCCTTATCAAGAGAAAAAATTGAAGCTTTAACAGAAATATGCAAACAAATGGAAGAGGAGGGAAAATTATCTAGGATAGGAGGAGAAAATCCTTATAATACACCAGTGTTTGCCATAAAGAAAAAGGATAAAACACAATGGAGAATGCTTGTAGATTTCAGGGAACTAAACAAAGCTACTCAAGACTTTTTTGAGGTTCAGCTGGG

AATTCCTCACCCAGCGGGCCTTCAGAAAAAGAAGCAAATCACAGTAATAGACATAGGGGATGCCTATTATTCAATACCATTATGCAAGGAATTCAGAAAATATACAGCATTTACCATCCCCTCAGTAAATAATACAGGGCCAGGGATAAGGTATCAGTTCAATTGTCTGCCTCAGGGATGGAAAGGATCTCCTACAATTTTCCAGAATACGGCAGCAAACATTTTAGAGGAGATCAAAAGGCACACTCCTGGGTTAGAAATTGTCCAATACATGGACGATTTGTGGTTGGCGTCAGACCATGATGAGACTAGACATAATCAACAGGTAGACATAGTAAGAAAGATGCTGCTAGAAAAAGGTCTAGAAACCCCAGACAAGAAAGTCCAAAGAGAACCGCCATGGGAATGGATGGGGTATAAATTGCATCCGAATAAATGGACCATTAACAAAATAGAATTACCCCCCTTAGAAGGAGAATGGACAGTAAACAAAATACAGAAGGTAGTAGGAGTTCTAAATTGGGCAAGTCAAATTTATCCAGGAATTAAAACCAAACATACCTGTGCCATGTTGAGAGGGAAAAAGAACCTCCTAGAAGAAATAGTATGGACAGAAGAGGCAGAGGCAGAATATAAGAACAATCAAGGGATAGTGCAGGAAACACAAGAAGGAACATACTATGACCCTCTCAAAGAATTAATAGCAACAGTTCAAAAGCAAGGAGAAGGGCAATGGACATACCAATTCACCCAAGAAGGGGCAGTATTAAAGGTGGGAAGATATGCCAAGCAAAGAGAAACTCATACTAATGATCTAAGGACTCTAGCACACCTTGTCCAAAAAATCTGTAAGGAAGCACTTACCATTTGGGGAAGACTTCCACGAGTACAACTCCCAGTAGACAAGAAAACATGGGATATGTGGTGGCAGGACTATTGGCAAGTATCCTGGATACCAGAATGGGAGTTTGTTAGCACACCACTCCTAGTAAAACTGTGG

TATTCCTTAGTAAAAGAACCAATCAAAGGAGAAGATGTTTATTATGTGGATGGGGCAGCATCCAAAGTGACCAAATTAGGTAAGGCAGGATATCTGTCAGAGAGAGGAAAAAGTAGAATTAGGGAATTAGAAAACACCACTAACCAACAAGCAGAATTAACAGCAGTTAAGATGGCATTGGAGGACAGTGGAGAAAATGTAAATATAGTCACAGATTCTCAATATGTAATGAACATCTTGACAGCATGTCCACAGGAAAGTAACTCACCCTTAGTGGAACAGATAATACAAGCCCTAATGAAAAAGAGGCAGGTCTACTTACAATGGGTACCAGCTCATAAGGGGATAGGAGGCAATACAGAAATAGATAAATTAGTAAGCAAAGGAATAAGACAGATCCTCTTCTTAGATAGAATAGAAGAAGCACAAGATGACCATGCAAAGTACCATAACAATTGGAGAAGTATGGTACAGGAATTTGGATTACCTAATATAGTAGCAAAAGAGATAGTAGCGGCATGTCCCAAATGCCAAATAAGAGGAGAACCTAAGCATGGACAGGTAGACGCCTCCATTGAAACTTGGCAGATGGACTGCACCCATTTAGAAGGAAAAGTTATAATAGTAGCAGTACATGTAGCCAGTGGATTCATAGAAGCAGAGGTGATCCCAAGAGAAACTGGGAAGGAGACAGCACACTTTCTGCTGAAACTGTTAGCAAGATGGCCAGTGAAACATCTACACACTGATAATGGCCCAAACTTTACCTCTCAGAATGTGGCAGCGGTGTGCTGGTGGGGTAATATAGAGCACACCACTGGAATACCTTATAACCCACAGTCACAGGGTAGTGTAGAAAGCATGAACAGACAGCTCAAGGAAATCATCTCTCAAATAAGAGATGATTGTGAGAGATTGGAGACAGCAGTGCAAATGGCTACGCATATCCACAATTTTAAAAGAAAGGGAGGAATAGGGGGTATCTCTAGTGCAGAAAGAT

TGGTTAATATGCTAACAACACAACTAGAACTAAATACTCTACAAAACCAAATCCAAAAAATTTTGAATTTTAAGGTCTACTACAGAGAAGGTAGAGATCCAGTGTGGAAAGGACCAGCGCGACTCATCTGGAAAGGAGAAGGCGCGGTGGTAATTAAAGAGGGGGAAGACATCAAGGTAGTCCCCAGGAGAAAGGCTAAGATTATCAAAGATTATGGAGAGAGAAAAACAATGGATAGTGAGGGTAGTATGGAGGGTGTCAGAGAGGCAAATAAGCAGATGGAGGGGGATAGTGACTTACAAGATCAGGAATAAACAATTGCCTTGGGAATACAGACATCATTGGCAGGTGCAATGGCAGTTTTGGACCTACAGCCAGTTCATTATCCCCTTATCAAAAGATGATTACATAGAAGTGAATATTTATCACAACCTCACCCCAGAAAGAGGATGGCTCTCAAGTCATGGAGTAGGGTTATCCTATTACCATCAAAAGGGATATAAGACAGAAGTAGATCCAGGAACAGCAGACAGAATGATACACCTATATTATTTTAACTGTTTTACAGATAGAGCCATCCAACAGGCTATCAGAGGGGAGAAGTATACGTGGTGCACATTCAAGGAAGGACATAAAGGTCAGGTACAATCACTGCAACTTTTGGCACTAGTTGCATATACAAATGGCATCAGGAAGAGATCCAAGAGAACCTTTACCAGGATGGCTGGAAATCTGGGATCTAGACAGGGAGCCATGGGACGAATGGCTACAAGACATGCTCAGGGATCTAAACGAAGAAGCCAGAAGGCACTTTGGAATGAACATGCTAATCCGAGTATGGAATTACTGTGTAGAGGAGGGAAGGAGACATAATACCCCATGGAATGAGATAGGCTACAAGTACTATAGAATTGTTCAAAAGTCTATGTTTGTACATTTCAGATGTGGTTGTAGAAGGAGAGGACCTTTTTCCCCTTACGAAGAGAGGAGAAATGGACAA

GGAGGAGGAGCCCCACCCCCTCCTCCAGGACTTGCATAGGCCATTACAACCATGTACTAATAAATGCTATTGCAAAAAATGCTGTTATCACTGTGAGCTTTGCTTCCTGCAGAAGGGCTTAGGAGTGCGTTATCATGTCTCTAGGAAAAGAAGAAAAACAAGCACTCAAGATAATCAAGACCCTATACGGCAGCAGTAAGTATGGGGAGATTGCTTATAAAAATACTAATAATAGCAATAGGGATAAGTATAGGAATAGGTAACCTGTATGTGACAGTGTTTTATGGAATCCCAGTATGGAAAAATTCAACAGTTCAGGCATTTTGCATGACGCCCAATACCAATATGTGGGCAACCACCAACTGCATACCAGATGATCATGATAATACAGAGGTGCCTCTAAACATTACAGAAGCTTTCGAGGCTTGGGATAATCCGCTGGTAAAACAAGCAGAGAGTAATATACATCTACTCTTTGAACAAACGATGAGGCCTTGTGTTAAGCTCTCCCCCATATGTATTAAAATGTCCTGTGTAGAGCTGAATGGTACAGCCACGACAAAGGCCACCACTACTGCAACTACAACAATGACTACCCCCTGTCAGAATTGCAGTACAGAGCAGATAGAAGGAGAAATGGCAGAGGAACCAGCATCCAACTGCACTTTTGCAATTGCAGGATATCAAAGAGATGTAAAAAAGAATTATAGCATGACCTGGTATGATCAGGAGTTAGTCTGCAATAATAAAACAGGAAGTGAAAAGGGAAGTAAGGATTGTTACATGATACATTGTAATGATTCAGTGATAAAAGAAGCTTGTGATAAAACATATTGGGATACTTTAAGAGTAAGATACTGTGCACCAGCAGGGTATGCTTTGCTAAAATGTAATGATAAGGATTATAGAGGCTTTGCTCCAAAGTGCAAGAATGTTTCAGTAGTGCATTGTACTAGATTAATCAATACTACTATAACTACAGGGATAGGATTAAATGGTA

GTAGATCAGAAAATAGAACAGAGATATGGCAGAAAGGAGGAAATGATAATGATACAGTTATAATAAAGTTGAATAAGTTTTACAACTTGACAGTGAGATGCCGAAGACCTGGTAATAAAACAGTGTTGCCAGTAACAATCATGGCAGGGTTAGTATTTCACTCTCAGAAATATAATACCAGGTTAAAACAAGCGTGGTGCCACTTCCAAGGAGATTGGAAAGGGGCATGGAAAGAAGTCAGAGAAGAAGTAAAGAAAGTGAAAAATCTTACAGAAGTAAGCATAGAAAATATACATCTGAGAAGGATATGGGGAGATCCAGAATCAGCGAATTTTTGGTTCAATTGTCAAGGTGAATTTTTCTATTGTAAGATGGACTGGTTTATCAATTATCTAAACAATCGAACAGAAGATGCAGAAGGTACTAATAGGACCTGTGACAAAGGGAAGCCAGGACCAGGACCATGTGTTCAGAGAACTTATGTTGCCTGCCATATACGACAAGTAGTAAATGATTGGTACACTGTCTCTAAAAAGGTATATGCTCCACCAAGGGAAGGTCATTTGGAGTGTAACTCATCAGTCACGGCACTATACGTGGCAATAGATTATAACAACAAGTCTGGCCCAATAAATGTGACCCTAAGTCCTCAGGTACGCAGCATATGGGCGTACGAACTGGGAGACTATAAATTAGTAGAGATAACACCAATTGGCTTTGCTCCTACAGATGTAAGAAGATATACTGGCCCCACAAGAGAAAAAAGGGTGCCATTCGTGCTAGGGTTTCTAGGCTTCTTGGGAGCTGCTGGAACTGCAATGGGCGCAGCGGCAACAACGCTGACAGTCCAGTCTCGGCATTTGCTTGCTGGGATATTGCAGCAGCAGAAGAACTTGCTGGCGGCTGTGGAACAGCAACAACAGTTGTTGAAGCTGACCATTTGGGGTGTGAAAAACCTCAATGCCCGCGTCACAGCTCTCGAGAAGTACCTAGAGGATCA

GGCACGGCTAAATTCATGGGGATGTGCGTGGAAACAAGTATGTCACACCACAGTGCCATGGAAGTATAATAACACTCCTAAGTGGGACAATATGACTTGGTTGGAGTGGGAGAGACAAATTAATGCCTTGGAAGGCAACATAACTCAACTATTGGAAGAAGCACAAAATCAGGAATCAAAGAATCTGGATCTGTACCAGAAATTGGATGATTGGTCAGGGTTCTGGTCATGGTTCTCACTGTCAACTTGGTTAGGCTATGTTAAAATAGGATTTTTAGTGATAGTGATTATTCTAGGATTAAGATTTGCATGGGTATTATGGGGATGTATCAGAAATATTAGGCAGGGATATAATCCTCTCCCCCAGATCCATATCCACAGTTCAGCGGAACGGCCAGACAACGGAGGAGGGCAAGACAGAGGTGGAGAAAGCAGCAGCAGCAAATTGATAAGATTGCAGGAAGAGTCCTCAACACCTTCGAGGATCAACAACTGGTGGCTCAACTTCAAGAGCTGCAGCTTGAGAATAAGGACTTGGTGTTACAACATCTGCCTGACCCTCCTCATATTCATCAGGACAGCAGTGGGATACCTGCAGTATGGGCTCCAGCAACTCCAAGAGGCAGCAACAGGGCTTGCTCAAGCTCTGGCGAGGGCTGCGAGGGAAGCCTGGGGCAGACTGGGTGCTATTGTCCGATCCGCTTATCGGGCAGTCATCAACAGTCCAAGAAGAGTGCGGCAAGGCCTTGAAAAAGTCCTGGGGTAAAGGTAAAATGACTCCAGACGGCCGCCGCCTGCAAGAAGGAGACACCTTTGATGAGTGGGATGATGATGAAGAAGAAGTAGGCTTCCCTGTGCAACCTCGAGTCCCCTTAAGACAGATGACCTATAAATTAGCAGTGGACTTTTCCCACTTTTTAAAATCAAAGGGGGGACTGGATGGGATATATTACTCTGAAAGAAGAGAAAAGATCCTGAATTTGTATGCCTTGAACGAGTG

GGGAATAATAGATGATTGGCAAGCTTACTCACCAGGCCCGGGGATAAGGTACCCGAGAGTCTTTGGCTTCTGCTTTAAGCTAGTCCCAGTGGACCTGCATGAGGAGGCACGCAACTGTGAGAGACACTGTCTGATGCATCCAGCACAGATGGGGGAAGATCCTGATGGAATAGATCATGGAGAAGTCTTGGTCTGGAAGTTTGACCCGAAGTTGGCGGTGGAGTACCGCCCGGACATGTTTAAGGACATGCACGAACATGCAAAGCGCTAGTGTCAGCACTTTGCGGTTGGGACTTTCCGCCAGGGACTTTCCACAGTGGGTGGATCGGAGGCGGTACAGGGGCGGTACTGGGAGTGGCTTTCCCCTCAGAGCTGCATAAAAGCAGATGCTCGCTGGCTTGTAACTCAGTCTCTTACTAGGAGACCAGCTAGAGCCTGGGTGTTCGCTGGTTAGCCTAACCCGGTTGGCCACCGGGGGTAAGGACTCCTTGGCTTCATATAGCTCAATAAACCTGCTCGCTTAGTCGCTATATTGGAGTCAAGTGCTCATTGCTGCGCCGAGCCTCTAGAGGTGAACCTCTCTTACTGGGTTCTCCTGTACCCAGGTGGGAGAAACTCCAGCA

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..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................AGATGCTAAATGCCATAGGAGGACACCAAGGGGCTTTACAAGTGTTGAAGGAAGTAATCAATGAGGAAGCAGCAGARTGGGATAGAACTCATCCACCAGCAATGGGGCCRTTACCACCAGGGCAGCTAAGAGATCCG.....................................................................................................................................................................................................................................................................................................................................................................................................................

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gag-pol_2

MGGGHSALSGRSLDTFEKIRLRPNGKKKYQIKHLIWAGKEMERFGLHEKLLETKEGCQKIIEVLTPLEPTGSEGLKALFNLCCVIWCIHAEQKVKDTEEAVVTVKQHYHLVDKNEKAAKKKNETTAPPGGESRNYPVVNQNNAWVHQPLSPRTLNAWVKCVEEKRWGAEVVPMFQALSEGCLSYDVNQMLNVIGDHQGALQILKEVINEEAAEWDRTHRPPAGPLPAGQLRDPTGSDIAGTTSSIQEQIEWTFNANPRIDVGAQYRKWVILGLQKVVQMYNPQKVLDIRQGPKEPFQDYVDRFYKALRAEQAPQDVKNWMTQTLLIQNANPDCKLILKGLGMNPTLEEMLIACQGVGGPQHKAKLMVEMMSNGQNMVQVGPQKKGPRGPLKCFNCGKFGHMQRECKAPRQIKCFKCGKIGHMAKDCKNGQANFF

LGYGHWGGAKPRNFVQYRGDTVGLEPTAPPMETAYDPAKKLLQQYAEKGQRLREEREQTRKQKEKEVEDVSLSSLFGGDQ*

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

gag-pol_1

RVWPLGRSETKKFCAIQRRHSWSGTNSPPNGNSLRSSKEAPPAVCREGTAPERGERTDKETEGERSGGCFLELPLWRRPMKRVIIEGTPVQALLDTGADDTIIQEKDLHFPPHKPWRSKVVGGIGGGIHVKEYQGVQVQLEDKIITGSILIGSTPINIIGRNILAQAGMKLVMGVLSSQIEETKVQLKEGKDGPKLKQWPLSREKIEALTEICKQMEEEGKLSRIGGENPYNTPVFAIKKKDKTQWRMLVDFRELNKATQDFFEVQLGIPHPAGLQKKKQITVIDIGDAYYSIPLCKEFRKYTAFTIPSVNNTGPGIRYQFNCLPQGWKGSPTIFQNTAANILEEIKRHTPGLEIVQYMDDLWLASDHDETRHNQQVDIVRKMLLEKGLETPDKKVQREPPWEWMGYKLHPNKWTINKIELPPLEGEWTVNKIQKVVGVLNWASQIYPGIKTKHTCAMLRGKKNLLEEIVWTEEAEAEYKNNQGIVQETQEGTYYDPLKELIATVQKQGEGQWTYQFTQEGAVLKVGRYAKQRETHTNDLRTLAHLVQKICKEALTIWGRLPRVQLPVDKKTWDMWWQDYWQVSWIPEWEFVSTPLLVKLWYSLVKEPIKGEDVYYVDGAASKVTKLGKAGYLSERGKSRIRELENTTNQQAELTAVKMALEDSGENVNIVTDSQYVMNILTACPQESNSPLVEQIIQALMKKRQVYLQWVPAHKGIGGNTEIDKLVSKGIRQILFLDRIEEAQDDHAKYHNNWRSMVQEFGLPNIVAKEIVAACPKCQIRGEPKHGQVDASIETWQMDCTHLEGKVIIVAVHVASGFIEAEVIPRETGKETAHFLLKLLARWPVKHLHTDNGPNFTSQNVAAVCWWGNIEHTTGIPYNPQSQGSVESMNRQLKEIISQIRDDCERLETAVQMATHIHNFKRKGGIGGISSAERLVNMLTTQLELNTLQNQIQKILNFKVYYREGRDPVWKGPARLIWKGEGAVVIKEGEDIKVVPRRKA

KIIKDYGERKTMDSEGSMEGVREANKQMEGDSDLQDQE*

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

vif

MEREKQWIVRVVWRVSERQISRWRGIVTYKIRNKQLPWEYRHHWQVQWQFWTYSQFIIPLSKDDYIEVNIYHNLTPERGWLSSHGVGLSYYHQKGYKTEVDPGTADRMIHLYYFNCFTDRAIQQAIRGEKYTWCTFKEGHKGQVQSLQLLALVAYTNGIRKRSKRTFTRMAGNLGSRQGAMGRMATRHAQGSKRRSQKALWNEHANPSMELLCRGGKET*

vpx

MASGRDPREPLPGWLEIWDLDREPWDEWLQDMLRDLNEEARRHFGMNMLIRVWNYCVEEGRRHNTPWNEIGYKYYRIVQKSMFVHFRCGCRRRGPFSPYEERRNGQGGGAPPPPPGLA*

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

env

MGRLLIKILIIAIGISIGIGNLYVTVFYGIPVWKNSTVQAFCMTPNTNMWATTNCIPDDHDNTEVPLNITEAFEAWDNPLVKQAESNIHLLFEQTMRPCVKLSPICIKMSCVELNGTATTKATTTATTTMTTPCQNCSTEQIEGEMAEEPASNCTFAIAGYQRDVKKNYSMTWYDQELVCNNKTGSEKGSKDCYMIHCNDSVIKEACDKTYWDTLRVRYCAPAGYALLKCNDKDYRGFAPKCKNVSVVHCTRLINTTITTGIGLNGSRSENRTEIWQKGGNDNDTVIIKLNKFYNLTVRCRRPGNKTVLPVTIMAGLVFHSQKYNTRLKQAWCHFQGDWKGAWKEVREEVKKVKNLTEVSIENIHLRRIWGDPESANFWFNCQGEFFYCKMDWFINYLNNRTEDAEGTNRTCDKGKPGPGPCVQRTYVACHIRQVVNDWYTVSKKVYAPPREGHLECNSSVTALYVAIDYNNKSGPINVTLSPQVRSIWAYELGDYKLVEITPIGFAPTDVRRYTGPTREKRVPFVLGFLGFLGAAGTAMGAAATTLTVQSRHLLAGILQQQKNLLAAVEQQQQLLKLTIWGVKNLNARVTALEKYLEDQARLNSWGCAWKQVCHTTVPWKYNNTPKWDNMTWLEWERQINALEGNITQLLEEAQNQESKNLDLYQKLDDWSGFWSWFSLSTWLGYVKIGFLVIVIILGLRFAWVLWGCIRNIRQGYNPLPQIHIHSSAERPDNGGGQDRGGESSSSKLIRLQEESSTPSRINNWWLNFKSCSLRIRTWCYNICLTLLIFIRTAVGYLQYGLQQLQEAATGLAQALARAAREAWGRLGAIVRSAYRAVINSPRRVRQGLEKVLG*

nef

MGSSNSKRQQQGLLKLWRGLRGKPGADWVLLSDPLIGQSSTVQEECGKALKKSWGKGKMTPDGRRLQEGDTFDEWDDDEEEVGFPVQPRVPLRQMTYKLAVDFSHFLKSKGGLDGIYYSERREKILNLYALNEWGIIDDWQAYSPGPGIRYPRVFGFCFKLVPVDLHEEARNCERHCLMHPAQMGEDPDGIDHGEVLVWKFDPKLAVEYRPDMFKDMHEHAKR*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	1459	1595	1.4%	158	57.7%	137 (100%)	107 (78.1%)	0/0
Mutations:	1466C>A 1471T>C 1472A>C 1480A>G 1481C>A 1484T>C 1487G>A 1493A>T 1500A>G 1502T>G 1503C>T 1505T>G 1514C>A 1517T>C 1523A>G 1535G>R 1541C>T 1544G>A 1547A>T 1550C>T 1551A>C 1552G>C 1557C>G 1560G>A 1561C>T 1562T>G 1565C>G 1568G>R 1575G>C 1592C>T
CDS

gag-pol_1	189	233	3.1%	288	84.5%	45 (100%)	38 (84.4%)	0/0/0/0	0
Protein mutations:	V192A (1471T>C 1472A>C) D195G (1480A>G 1481C>A) I202V (1500A>G 1502T>G) R219P (1551A>C 1552G>C) P221A (1557C>G) A222M (1560G>A 1561C>T 1562T>G) A227P (1575G>C)
Codon mutations:	CTC190CTA (1466C>A) GTA192GCC (1471T>C 1472A>C) GAC195GGA (1480A>G 1481C>A) CAT196CAC (1484T>C) CAG197CAA (1487G>A) GCA199GCT (1493A>T) ATT202GTG (1500A>G 1502T>G) CTT203TTG (1503C>T 1505T>G) GTC206GTA (1514C>A) ATT207ATC (1517T>C) GAA209GAG (1523A>G) GAG213GAR (1535G>R) GAC215GAT (1541C>T) AGG216AGA (1544G>A) ACA217ACT (1547A>T) CAC218CAT (1550C>T) AGA219CCA (1551A>C 1552G>C) CCA221GCA (1557C>G) GCT222ATG (1560G>A 1561C>T 1562T>G) GGC223GGG (1565C>G) CCG224CCR (1568G>R) GCA227CCA (1575G>C) GAC232GAT (1592C>T)
gag-pol_2	189	233	8.8%	288	84.5%	45 (100%)	38 (84.4%)	0/0/0/0	0
Protein mutations:	V192A (1471T>C 1472A>C) D195G (1480A>G 1481C>A) I202V (1500A>G 1502T>G) R219P (1551A>C 1552G>C) P221A (1557C>G) A222M (1560G>A 1561C>T 1562T>G) A227P (1575G>C)
Codon mutations:	CTC190CTA (1466C>A) GTA192GCC (1471T>C 1472A>C) GAC195GGA (1480A>G 1481C>A) CAT196CAC (1484T>C) CAG197CAA (1487G>A) GCA199GCT (1493A>T) ATT202GTG (1500A>G 1502T>G) CTT203TTG (1503C>T 1505T>G) GTC206GTA (1514C>A) ATT207ATC (1517T>C) GAA209GAG (1523A>G) GAG213GAR (1535G>R) GAC215GAT (1541C>T) AGG216AGA (1544G>A) ACA217ACT (1547A>T) CAC218CAT (1550C>T) AGA219CCA (1551A>C 1552G>C) CCA221GCA (1557C>G) GCT222ATG (1560G>A 1561C>T 1562T>G) GGC223GGG (1565C>G) CCG224CCR (1568G>R) GCA227CCA (1575G>C) GAC232GAT (1592C>T)
Proteins

Gag-Pol (NP_687035.1)	189	233	3.1%	288	84.5%	45 (100%)	38 (84.4%)	0/0/0/0	0
Protein mutations:	V192A (1471T>C 1472A>C) D195G (1480A>G 1481C>A) I202V (1500A>G 1502T>G) R219P (1551A>C 1552G>C) P221A (1557C>G) A222M (1560G>A 1561C>T 1562T>G) A227P (1575G>C)
Codon mutations:	CTC190CTA (1466C>A) GTA192GCC (1471T>C 1472A>C) GAC195GGA (1480A>G 1481C>A) CAT196CAC (1484T>C) CAG197CAA (1487G>A) GCA199GCT (1493A>T) ATT202GTG (1500A>G 1502T>G) CTT203TTG (1503C>T 1505T>G) GTC206GTA (1514C>A) ATT207ATC (1517T>C) GAA209GAG (1523A>G) GAG213GAR (1535G>R) GAC215GAT (1541C>T) AGG216AGA (1544G>A) ACA217ACT (1547A>T) CAC218CAT (1550C>T) AGA219CCA (1551A>C 1552G>C) CCA221GCA (1557C>G) GCT222ATG (1560G>A 1561C>T 1562T>G) GGC223GGG (1565C>G) CCG224CCR (1568G>R) GCA227CCA (1575G>C) GAC232GAT (1592C>T)
gag protein (NP_054369.1)	189	233	8.8%	288	84.5%	45 (100%)	38 (84.4%)	0/0/0/0	0
Protein mutations:	V192A (1471T>C 1472A>C) D195G (1480A>G 1481C>A) I202V (1500A>G 1502T>G) R219P (1551A>C 1552G>C) P221A (1557C>G) A222M (1560G>A 1561C>T 1562T>G) A227P (1575G>C)
Codon mutations:	CTC190CTA (1466C>A) GTA192GCC (1471T>C 1472A>C) GAC195GGA (1480A>G 1481C>A) CAT196CAC (1484T>C) CAG197CAA (1487G>A) GCA199GCT (1493A>T) ATT202GTG (1500A>G 1502T>G) CTT203TTG (1503C>T 1505T>G) GTC206GTA (1514C>A) ATT207ATC (1517T>C) GAA209GAG (1523A>G) GAG213GAR (1535G>R) GAC215GAT (1541C>T) AGG216AGA (1544G>A) ACA217ACT (1547A>T) CAC218CAT (1550C>T) AGA219CCA (1551A>C 1552G>C) CCA221GCA (1557C>G) GCT222ATG (1560G>A 1561C>T 1562T>G) GGC223GGG (1565C>G) CCG224CCR (1568G>R) GCA227CCA (1575G>C) GAC232GAT (1592C>T)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43