Genome Detective

NGS Details (SRR3458562_Metagenome_example): Feline leukemia virus

Assembly

Coverage Length

139 (1 contig(s))

Depth Of Coverage

1.5

Number Of Reads

Reads Per Million

0.13 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

Feline leukemia virus (Taxonomy ID: 11768)

Reference Genome

NC_001940.1

NT Identity (%)

80.8824

AA Identity (%)

76.087

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

156.0 (NT) + 259.0 (AA) = 415.0

Concordance (%)

73.4513

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 5392 and ends at position 5530 relative to NC_001940.1 reference sequence.

NC_001940.1

SRR3458562_Metagenome_example-NC_001940.1-77-0

NC_001940.1

SRR3458562_Metagenome_example-NC_001940.1-77-0

NC_001940.1

SRR3458562_Metagenome_example-NC_001940.1-77-0

TGAAAGACCCCCTACCCCAAAATTTAGCCAGCTACTGCAGTGGTGCCATTTCACAAGGCATGGAAAATTACTCAAGTATGTTCCCATGAGATACAAGGAAGTTAGAGGCTAAAACAGGATATCTGTGGTTAAGCACCTGGGCCCCGGCTTGAGGCCAAGAACAGTTAAACCCCGGATATAGCTGAAACAGCAGAAGTTTCAAGGCCGCTACCAGCAGTCTCCAGGCTCCCCAGTTGACCAGGGTTCGACCTTCCGCCTCATTTAAACTAACCAATCCCCACGCCTCTCGCTTCTGTGCGCGCGCTTTCTGCTATAAAACGAGCCATCAGCCCCCAACGGGCGCGCAAGTCTTTGCTGAGACTTGACCGCCCCGGGTACCCGTGTACGAATAAACCTCTTGCTGATTGCATCTGACTCGTGGTCTCGGTGTTCTGTGGGCGCGGGGTCTCATCGCCGAGGAAGACCTAGTTCAGGGGTCTTTCATTTGGGGGCTCGTCCGGGATCGAGACCCCCGACCCCCGGGACCACCGACCCACCATCAGGAGGTAAGCTGGCCGGCGACCATACCTGTTGTCCTTGTATAAGTGTCTCTGTCAATTGATCTGATTTTGGCGGTGGGATCGAAGGAGCTGACGAGCTCGTACTTCGCCCCCGCAACCCTGGAAGACGTTCCACGGGTGTCTGATGTCTGGAGCCTCTAGTGGGACAGCCATTGGGGCTCATCTGTTTGGGGTCTCACCTGAATACAGGGTGTTGATCGGAGACGAGGGAGCCGGACCCTCAAAGTCTCTTTCTGAGGTTTCATTTTCGGTTTGGTACCGAAGCCGCGCGGCACGTCTTGTCATTTTTTGTCTGGTTGCGTCTTTTCTTGTCCCTTGTCTAACCTTTTTAATTGCAGAAACCGTCATGGGCCAAACTATAACTACCCCCTTAAGCCTCACCCTTGATCACTGGTCTGAAGTCCGGGCACGAGCCCATAACCAAGGTGTCGAGGTCCGGA

AAAAGAAATGGATTACCTTATGTGAGGCCGAATGGGTGATGATGAATGTGGGCTGGCCCCGAGAGGGAACTTTTTCTCTTGATAACATTTCCCAGGTTGAGAAAAAGATCTTCGCCCCGGGACCGTATGGACACCCCGACCAGGTTCCTTACATTACCACATGGAGATCCTTAGCCACAGACCCCCCTTCGTGGGTTCGGCCGTTCCTACCCCCTCCCAAACCTCCCACGCCCCTCCCTCAACCTCTCTCGCCGCAGCCCTCCGCCCCTCTTACCTCTTCCCTCTACCCCGTCCTCCCCAAGTCAGACCCTCCCAAACCGCCTGTGTTACCGCCTGATCCTTCTTCCCCTTTAATAGATCTCTTAACAGAAGAGCCACCTCCCTATCCGGGAGGTCACGGGCCACCGCCGTCAGGTCCTAGGACCCCAACCGCTTCCCCGATTGCAAGCCGGCTAAGGGAACGACGAGAAAACCCTGCTGAAGAATCTCAAGCCCTCCCCTTGAGGGAGGGCCCCAACAACCGACCCCAGTATTGGCCATTCTCAGCCTCAGACCTGTATAACTGGAAGTCGCATAACCCCCCTTTCTCCCAAGACCCAGTGGCCCTAACTAACCTAATTGAGTCCATTTTAGTGACGCATCAACCAACCTGGGACGACTGCCAGCAGCTCTTGCAGGCACTCCTGACAGGCGAAGAAAGGCAAAGGGTCCTTCTTGAGGCCCGAAAGCAGGTTCCAGGCGAGGACGGACGGCCAACCCAACTACCCAATGTCATTGATGAGACTTTCCCCTTGACCCGTCCCAACTGGGATTTTGCTACGCCGGCAGGTAGGGAGCACCTACGCCTTTATCGCCAGTTGCTATTAGCGGGTCTCCGCGGGGCTGCAAGACGCCCCACTAATTTGGCACAGGTAAAGCAGGTTGTACAAGGGAAAGAGGAAACGCCAGCAGCATTTTTAGAAAGATTAAAAGAGGCTTACAGAATGTACACTCCCTATGA

CCCTGAGGACCCAGGGCAAGCAGCTAGTGTTATACTATCCTTTATATACCAGTCTAGCCCAGATATAAGAAATAAGTTACAAAGGCTAGAAGGTCTACAAGGGTTCACCCTATCTGATCTGCTAAAAGAGGCAGAAAAGATATACAACAAAAGGGAGACCCCAGAGGAAAGGGAAGAAAGATTATGGCAGCGGCAAGAAGAAAGAGATAAAAAGCGCCACAAGGAGATGACTAAAGTTCTGGCCACAGTAGTTGCTCAGAATAGAGATAAAGATAGAGAAGAAAGTAAACTGGGGGATCAAAGGAAAATACCTCTGGGAAAGGACCAGTGTGCCTATTGCAAGGAAAAGGGGCATTGGGTTCGCGATTGCCCCAAACGACCCCGGAAGAAACCCGCCAACTCCACTCTCCTCAACTTAGGAGATTAGGAGAGTCAGGGCCAGGACCCCCCCCCTGAGCCCAGGATAACCTTAAAAATAGGGGGGCAACCGGTGACTTTCCTGGTGGACACGGGAGCCCAGCACTCAGTACTAACTCGACCAGATGGACCTCTCAGTGACCGCACAGCCCTGGTGCAAGGAGCCACGGGAAGCAAAAACTACCGGTGGACCACCGACAGGAGGGTACAACTGGCAACCGGTAAGGTGACTCATTCTTTTTTATATGTACCTGAATGTCCCTACCCGTTATTAGGGAGAGACCTATTAACTAAACTTAAGGCCCAAATCCATTTTACCGGAGAAGGGGCTAATGTTGTTGGGCCCAAGGGTTTACCCCTACAAGTCCTTACTTTACAATTAGAAGAGGAGTATCGGCTATTTGAGCCCGAAAGTACACAAAAACAGGAGATGGACATTTGGCTTAAAAACTTTCCCCAGGCGTGGGCAGAAACAGGAGGTATGGGAACGGCTCATTGTCAAGCCCCCGTTCTCATTCAACTTAAGGCTACTGCCACTCCAATCTCCATCCGACAGTATCCTATGCCCCATGAAGCATACCAG

GGAATTAAGCCTCATATAAGAAGAATGCTAGATCAAGGCATCCTCAAGCCCTGCCAGTCCCCATGGAATACACCCTTATTACCTGTTAAGAAGCCAGGGACCGAGGATTACAGACCAGTGCAGGACTTAAGAGAAGTAAACAAAAGAGTGGAAGACATCCATCCTACTGTGCCAAATCCATATAACCTCCTTAGCACCCTCCCGCCGTCTCACCCTTGGTACACTGTCCTAGATTTAAAAGACGCTTTTTTCTGCCTGCGACTACACTCTGAGAGTCAATTACTTTTTGCATTTGAATGGAGAGATCCAGAAATAGGACTGTCAGGGCAGCTAACCTGGACACGCCTTCCTCAAGGGTTCAAGAATAGCCCCACCCTATTTGATGAGGCCCTGCACTCAGACCTGGCCGATTTCAGGGTAAGGTACCCGGCTCTAGTCCTCCTACAATATGTAGATGACCTCTTGCTGGCTGCGGCAACCAGGACTGAATGCCTGGAAGGGACTAAGGCACTCCTTGAGACTTTGGGCAATAAGGGGTACCGAGCCTCTGCAAAGAAGGCCCAAATTTGCCTGCAAGAAGTCACATACCTGGGGTACTCTTTAAAAGATGGCCAAAGGTGGCTTACCAAAGCTCGCAAGGAAGCCATCCTATCCATCCCTGTGCCTAAAAACTCACGACAAGTAAGAGAGTTCCTTGGAACTGCAGGTTACTGCCGGCTGTGGATTCCCGGTTTTGCCGAGCTCGCAGCCCCGCTATACCCTCTCACTCGACCAGGAACTCTGTTCCAGTGGGGAACAGAGCAACAATTGGCCTTCGAGGACATTAAAAAAGCCCTCTTGAGTTCCCCTGCCCTGGGGTTGCCAGATATCACCAAACCCTTTGAATTATTTATTGATGAGAACTCAGGATTTGCAAAGGGGGTGTTAGTCCAAAAACTGGGACCCTGGAAAAGACCAGTTGCCTACCTATCAAAAAAGCTGGATACAGTGGCATCTGGAT

GGCCCCCTTGTTTACGCATGGTTGCAGCCATCGCCATCCTAGTCAAGGATGCAGGGAAGCTAACCCTAGGACAGCCGCTAACTATCCTGACCTCCCACCCAGTTGAGGCACTTGTCCGACAGCCTCCAAATAAATGGCTCTCTAATGCTAGAATGACTCATTACCAAGCTATGCTCCTCGATGCAGAGCGAGTCCATTTCGGGCCGACAGTCTCCCTTAACCCTGCTACCTTGCTCCCCCTCCCCAGCGGGGGAAACCACCACGACTGTCTCCAGATTTTAGCCGAGACCCATGGCACCAGACCCGACTTAACTGACCAGCCGTTGCCGGATGCAGACCTGACCTGGTACACAGATGGTAGCAGCTTCATCCGTAATGGCGAGAGAGAGGCCGGAGCCGCAGTAACAACCGAATCTGAGGTAATCTGGGCTGCTCCCCTCCCACCCGGAACGTCAGCCCAGCGAGCCGAACTGATTGCCCTGACCCAGGCACTAAAGATGGCAGAAGGTAAGAAGCTAACTGTCTATACGGACAGCCGATATGCCTTTGCTACAACTCATGTACACGGGGAAATCTACAGGCGGCGGGGCCTACTAACTTCAGAAGGAAAAGAAATTAAAAATAAAAATGAAATCCTCGCCCTACTAGAGGCGTTATTCTTACCCAAAAGACTGAGCATCATCCATTGCCCGGGACACCAAAAAGGTGATAGTCCCCAGGCAAAAGGAAACAGATTAGCTGATGATACAGCAAAGAAAGCCGCCACAGAGACTCATTCATCACTAACCGTCTTACCCACTGAACTTATAGAGGGTCCCAAAAGGCCTCCATGGGAATATGATGACAGTGATTTAGACCTTGTGCAAAAACTCGAAGCTCATTATGAGCCAAAGAGAGGTACCTGGGAGTACCGAGGAAAAACTATCATGCCTGAAAAATACGCAAAAGAGTTGATTAGCCATCTGCATAAGTTAACACACCTCAGTGCTAGGAAAATGAA

AACTTTACTAGAAAGAGAAGAAACTGGGTTTTACCTCCCTAACAGAGACTTACACCTCCGGCAAGTAACAGAGAGCTGCCGGGCATGTGCTCAAATCAACGCCGGAAAGATAAAGTTTGGACCTGATGTAAGGGCCCGAGGCCGCCGGCCCGGAACACATTGGGAAGTAGACTTCACTGAAATCAAGCCAGGAATGTATGGATATAAATACCTCTTGGTGTTCATAGATACCTTCTCTGGCTGGGCCGAAGCTTACCCCGCCAAACATGAAACAGCAAAAGTTGTTGCCAAGAAACTCTTAGAAGAAATTTTTCCCCGCTACGGGATCCCTCAGGTATTGGGTTCAGATAATGGACCCGCCTTTATCTCCCAGGTAAGTCAGTCTGTGGCCACCCTACTGGGGATTAATTGGAAGTTACATTGTGCATACCGACCCCAAAGTTCAGGTCAGGTAGAAAGAATGAATAGATCAATTAAGGAGACTTTAACTAAATTAACGCTAGAAACTGGCTCTAAGGATTGGGTGCTCCTCCTGCCCCTGGTTTTATACCGGGTACGTAACACGCCAGGCCCCCACGGGTTAACTCCTTTTGAAATCCTGTACGGGGCACCCCCACCTATGGCTCACTTCTTTGATACTGATATCTCTAGCTTCGCTACCTCCCCCACTATGCAGGCACATTTACGCGCCCTGCAGCTGGTCCAAGAAGAGATCCAGAGACCTCTAGCGGCGGCCTACCGAGAAAAACTTGAAACCCCGGTTGTGCCTCACCCCTTCAAACCAGGAGACTCCGTCTGGGTTCGGAGACATCAAACCAAGAACCTCGAGCCACGGTGGAAAGGACCACATATCGTCCTCCTGACCACCCCCACAGCCTTAAAGGTAGACGGAGTTGCTGCCTGGATTCACGCCTCTCACGTGAAAGCTGCAGGACCAACCACCAATCAAGACCTCTCGGACAGCCCCAGCTCAGACGATCCATCAAGATGGAAAGTCCAA

CGCACCCAAAACCCTCTAAAGATAAGACTCTCTCGTGGAACTTAGCGTTTCTGGTGGGGATCTTATTCACAATAGACATAGGAATGGCCAATCCTAGTCCACACCAAATATATAATGTAACTTGGGTAATAACCAATATGCAAACTAACACCCAAGCTAATGCCACCTCTATGTTAGGAACCTTAACCGATGCCTACCCTACCCTACATGTTGACCTATGTGACCTAGTGGGAGACACCTGGGAACCTATAGTCCTAGATCCAACCAATGTAAAACACGGGGCACGTTACTCCTCCTCAAAGTATGGATGTAAAACTACAGATAGAAAAAAACAGCAACAAACATACCCCTTTTACGTCTGCCCCGGACATGCCCCCTCGCTGGGGCCAAAGGGAACACATTGTGGAGGGGCACAAGATGGGTTTTGTGCCGCATGGGGATGTGAGACCACCGGAGAAGCTTGGTGGAAGCCCTCCTCCTCATGGGACTATATCACAGTAAAAAGAGGGAGTAGTCAGGACAATAGCTGTGAGGGAAAATGCAACCCCCTGATTTTGCAGTTCACCCAGAAGGGAAGACAAGCCTCTTGGGACGGACCTAAGATATGGGGATTGCGACTATACCGTACAGGATATGACCCTATCGCCTTATTCACGGTGTCCCGGCAGGTGTCAGCCATTACGCCGCCTCAGGCAATGGGACCAAACCTAGTCTTACCTGATCAAAAACCCCCATCCAGACAATCCCAAACAGGGTCCAAAGTGGCGACCCAGAGGCTCCAAACGACTGAAAGCGCCCCAAGGTCTGTTGCCCCCACCACCGTGGGTCCCAAACGGATTGGGACCGGAGATAGGTTAATAAATTTAGTACAAGGGACATACCTAGCCTTAAATGCCACCGACCCCAACAAAACTAAAGACTGTTGGCTCTGCCTGGTTTCTCGACCACCCTATTACGAAGGGATTGCAATCTTAGGTAACTACAGCAACCAAACAAACCC

CCCCCCATCCTGCCTATCTACTCCGCAACACAAACTGACCATATCTGAAGTATCAGGGCAAGGACTGTGCATAGGGACTGTTCCTAAGACCCACCAGGCTTTGTGCAATGAGACACAACAGGGACATACAGGGGCGCACTATCTAGCCGCCCCCAATGGCGCCTATTGGGCCTGTAACACTGGACTCACCCCATGCATTTCCATGGCGGTGCTCAATTGGACCTCTGATTTTTGTGTCTTAATCGAATTATGGCCCAGAGTGACTTACCATCAACCCGAATATGTGTACACACATTTTGCCAAAGCTGTCAGGTTCCGAAGAGAACCAATATCACTAACTGTTGCCCTCATGTTGGGAGGACTCACTGTAGGGGGCATAGCCGCGGGGGTCGGAACAGGGACTAAAGCCCTCCTTGAAACAGCCCAGTTCAGACAACTACAAATGGCCATGCACACAGACATCCAGGCCCTAGAAGAGTCAATTAGTGCCTTAGAAAAGTCCCTGACCTCCCTTTCTGAAGTAGTCTTACAAAACAGACGGGGCCTAGATATTCTATTCTTACAAGAGGGAGGGCTCTGTGCCGCATTAAAAGAAGAATGTTGCTTCTATGCGGATCACACCGGACTCGTCCGAGACAATATGGCTAAATTGAGAGAAAGACTAAAACAGCGGCAACAACTGTTTGACTCCCAACAGGGATGGTTTGAAGGATGGTTCAACAAGTCCCCCTGGTTCACAACCTTAATTTCCTCCATTATGGGCCCCTTACTAATCCTACTCCTAATTCTCCTCTTCGGCCCATGCATCCTTAACAGATTAGTACAATTCGTAAAAGACAGAATATCTGTGGTACAAGCCTTAATTTTAACCCAACAGTACCAACAGATAAAGCAATACGATCCGGACCGACCATGATTTCCAATTAAATGTATGATTCCATTTAGTCCCCAGAAAAAGGGGGGAATGAAAGACCCCCTACCCCAAAATTTAGCCAGCTAC

TGCAGTGGTGCCATTTCACAAGGCATGGAAAATTACTCAAGTATGTTCCCATGAGATACAAGGAAGTTAGAGGCTAAAACAGGATATCTGTGGTTAAGCACCTGGGCCCCGGCTTGAGGCCAAGAACAGTTAAACCCCGGATATAGCTGAAACAGCAGAAGTTTCAAGGCCGCTACCAGCAGTCTCCAGGCTCCCCAGTTGACCAGGGTTCGACCTTCCGCCTCATTTAAACTAACCAATCCCCACGCCTCTCGCTTCTGTGCGCGCGCTTTCTGCTATAAAACGAGCCATCAGCCCCCAACGGGCGCGCAAGTCTTTGCTGAGACTTGACCGCCCCGGGTACCCGTGTACGAATAAACCTCTTGCTGATTGCATCTGACTCGTGGTCTCGGTGTTCTGTGGGCGCGGGGTCTCATCGCCGAGGAAGACCTAGTTCAGGGGTCTTTCA

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.......................................................................................................................................................................................................................................................................................................................................................................................................ACCATACTTGGGGCTGATTGGAAATTACATTGTGCATACCGACCCCAAAGCTCAGGACAGGTAGAGAGAATGGACAGAATATTAAAGGAGACCCTAACCAAATTGACCATGGAGACTGGCACT---AATTGGGTGGTCC......................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

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gag-pro-pol

MSGASSGTAIGAHLFGVSPEYRVLIGDEGAGPSKSLSEVSFSVWYRSRAARLVIFCLVASFLVPCLTFLIAETVMGQTITTPLSLTLDHWSEVRARAHNQGVEVRKKKWITLCEAEWVMMNVGWPREGTFSLDNISQVEKKIFAPGPYGHPDQVPYITTWRSLATDPPSWVRPFLPPPKPPTPLPQPLSPQPSAPLTSSLYPVLPKSDPPKPPVLPPDPSSPLIDLLTEEPPPYPGGHGPPPSGPRTPTASPIASRLRERRENPAEESQALPLREGPNNRPQYWPFSASDLYNWKSHNPPFSQDPVALTNLIESILVTHQPTWDDCQQLLQALLTGEERQRVLLEARKQVPGEDGRPTQLPNVIDETFPLTRPNWDFATPAGREHLRLYRQLLLAGLRGAARRPTNLAQVKQVVQGKEETPAAFLERLKEAYRMYTPYDPEDPGQAASVILSFIYQSSPDIRNKLQRLEGLQGFTLSDLLKEAEKIYNKRETPEEREERLWQRQEERDKKRHKEMTKVLATVVAQNRDKDREESKLGDQRKIPLGKDQCAYCKEKGHWVRDCPKRPRKKPANSTLLNLGD*ESQGQDPPPEPRITLKIGGQPVTFLVDTGAQHSVLTRPDGPLSDRTALVQGATGSKNYRWTTDRRVQLATGKVTHSFLYVPECPYPLLGRDLLTKLKAQIHFTGEGANVVGPKGLPLQVLTLQLEEEYRLFEPESTQKQEMDIWLKNFPQAWAETGGMGTAHCQAPVLIQLKATATPISIRQYPMPHEAYQGIKPHIRRMLDQGILKPCQSPWNTPLLPVKKPGTEDYRPVQDLREVNKRVEDIHPTVPNPYNLLSTLPPSHPWYTVLDLKDAFFCLRLHSESQLLFAFEWRDPEIGLSGQLTWTRLPQGFKNSPTLFDEALHSDLADFRVRYPALVLLQYVDDLLLAAATRTECLEGTKALLETLGNKGYRASAKKAQICLQEVTYLGYSLKDGQRWLTKARKEAILSIPVPKNSRQV

REFLGTAGYCRLWIPGFAELAAPLYPLTRPGTLFQWGTEQQLAFEDIKKALLSSPALGLPDITKPFELFIDENSGFAKGVLVQKLGPWKRPVAYLSKKLDTVASGWPPCLRMVAAIAILVKDAGKLTLGQPLTILTSHPVEALVRQPPNKWLSNARMTHYQAMLLDAERVHFGPTVSLNPATLLPLPSGGNHHDCLQILAETHGTRPDLTDQPLPDADLTWYTDGSSFIRNGEREAGAAVTTESEVIWAAPLPPGTSAQRAELIALTQALKMAEGKKLTVYTDSRYAFATTHVHGEIYRRRGLLTSEGKEIKNKNEILALLEALFLPKRLSIIHCPGHQKGDSPQAKGNRLADDTAKKAATETHSSLTVLPTELIEGPKRPPWEYDDSDLDLVQKLEAHYEPKRGTWEYRGKTIMPEKYAKELISHLHKLTHLSARKMKTLLEREETGFYLPNRDLHLRQVTESCRACAQINAGKIKFGPDVRARGRRPGTHWEVDFTEIKPGMYGYKYLLVFIDTFSGWAEAYPAKHETAKVVAKKLLEEIFPRYGIPQVLGSDNGPAFISQVSQSVATLLGINWKLHCAYRPQSSGQVERMNRSIKETLTKLTLETGSKDWVLLLPLVLYRVRNTPGPHGLTPFEILYGAPPPMAHFFDTDISSFATSPTMQAHLRALQLVQEEIQRPLAAAYREKLETPVVPHPFKPGDSVWVRRHQTKNLEPRWKGPHIVLLTTPTALKVDGVAAWIHASHVKAAGPTTNQDLSDSPSSDDPSRWKVQRTQNPLKIRLSRGT*

.........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TILGADWKLHCAYRPQSSGQVERMDRILKETLTKLTMETGT-NWVVX...........................................................................................................................................................................

env

MESPTHPKPSKDKTLSWNLAFLVGILFTIDIGMANPSPHQIYNVTWVITNMQTNTQANATSMLGTLTDAYPTLHVDLCDLVGDTWEPIVLDPTNVKHGARYSSSKYGCKTTDRKKQQQTYPFYVCPGHAPSLGPKGTHCGGAQDGFCAAWGCETTGEAWWKPSSSWDYITVKRGSSQDNSCEGKCNPLILQFTQKGRQASWDGPKIWGLRLYRTGYDPIALFTVSRQVSAITPPQAMGPNLVLPDQKPPSRQSQTGSKVATQRLQTTESAPRSVAPTTVGPKRIGTGDRLINLVQGTYLALNATDPNKTKDCWLCLVSRPPYYEGIAILGNYSNQTNPPPSCLSTPQHKLTISEVSGQGLCIGTVPKTHQALCNETQQGHTGAHYLAAPNGAYWACNTGLTPCISMAVLNWTSDFCVLIELWPRVTYHQPEYVYTHFAKAVRFRREPISLTVALMLGGLTVGGIAAGVGTGTKALLETAQFRQLQMAMHTDIQALEESISALEKSLTSLSEVVLQNRRGLDILFLQEGGLCAALKEECCFYADHTGLVRDNMAKLRERLKQRQQLFDSQQGWFEGWFNKSPWFTTLISSIMGPLLILLLILLFGPCILNRLVQFVKDRISVVQALILTQQYQQIKQYDPDRP*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	5392	5530	1.6%	156	60.0%	136 (97.8%)	110 (79.1%)	0/3
Mutations:	5395C>A, 5400G>T, 5404A>G, 5405T>C, 5407A>G, 5415G>A, 5442T>C, 5448T>A, 5457A>G, 5464A>G, 5466T>C, 5470T>A, 5471C>T, 5473A>T, 5475T>A, 5484T>C, 5485T>C, 5490T>C, 5496A>G, 5499G>C, 5500C>A, 5502A>G, 5505A>G, 5512T>A, 5515_5517delAAG, 5518G>A, 5527C>G
CDS

gag-pro-pol	1570	1616	2.6%	259	83.8%	46 (97.9%)	35 (74.5%)	0/1/0/0	0
Protein mutations:	L1571I (5395C>A), I1574A (5404A>G 5405T>C), N1575D (5407A>G), N1594D (5464A>G 5466T>C), S1596I (5470T>A 5471C>T), I1597L (5473A>T 5475T>A), L1606M (5500C>A 5502A>G), S1610T (5512T>A), K1611del (5515_5517delAAG), D1612N (5518G>A), L1615V (5527C>G)
Codon mutations:	CTA1571ATA (5395C>A), CTG1572CTT (5400G>T), ATT1574GCT (5404A>G 5405T>C), AAT1575GAT (5407A>G), AAG1577AAA (5415G>A), AGT1586AGC (5442T>C), GGT1588GGA (5448T>A), GAA1591GAG (5457A>G), AAT1594GAC (5464A>G 5466T>C), TCA1596ATA (5470T>A 5471C>T), ATT1597TTA (5473A>T 5475T>A), ACT1600ACC (5484T>C), TTA1601CTA (5485T>C), ACT1602ACC (5490T>C), TTA1604TTG (5496A>G), ACG1605ACC (5499G>C), CTA1606ATG (5500C>A 5502A>G), GAA1607GAG (5505A>G), TCT1610ACT (5512T>A), AAG1611del (5515_5517delAAG), GAT1612AAT (5518G>A), CTC1615GTC (5527C>G)
Proteins

Gag-Pro-Pol precursor polyprotein gPr80 (NP_047255.1)	1570	1616	2.6%	259	83.8%	46 (97.9%)	35 (74.5%)	0/1/0/0	0
Protein mutations:	L1571I (5395C>A), I1574A (5404A>G 5405T>C), N1575D (5407A>G), N1594D (5464A>G 5466T>C), S1596I (5470T>A 5471C>T), I1597L (5473A>T 5475T>A), L1606M (5500C>A 5502A>G), S1610T (5512T>A), K1611del (5515_5517delAAG), D1612N (5518G>A), L1615V (5527C>G)
Codon mutations:	CTA1571ATA (5395C>A), CTG1572CTT (5400G>T), ATT1574GCT (5404A>G 5405T>C), AAT1575GAT (5407A>G), AAG1577AAA (5415G>A), AGT1586AGC (5442T>C), GGT1588GGA (5448T>A), GAA1591GAG (5457A>G), AAT1594GAC (5464A>G 5466T>C), TCA1596ATA (5470T>A 5471C>T), ATT1597TTA (5473A>T 5475T>A), ACT1600ACC (5484T>C), TTA1601CTA (5485T>C), ACT1602ACC (5490T>C), TTA1604TTG (5496A>G), ACG1605ACC (5499G>C), CTA1606ATG (5500C>A 5502A>G), GAA1607GAG (5505A>G), TCT1610ACT (5512T>A), AAG1611del (5515_5517delAAG), GAT1612AAT (5518G>A), CTC1615GTC (5527C>G)
Pol gene polyprotein (NP_955577.1)	994	1040	3.9%	259	83.8%	46 (97.9%)	35 (74.5%)	0/1/0/0	0
Protein mutations:	L995I (5395C>A), I998A (5404A>G 5405T>C), N999D (5407A>G), N1018D (5464A>G 5466T>C), S1020I (5470T>A 5471C>T), I1021L (5473A>T 5475T>A), L1030M (5500C>A 5502A>G), S1034T (5512T>A), K1035del (5515_5517delAAG), D1036N (5518G>A), L1039V (5527C>G)
Codon mutations:	CTA995ATA (5395C>A), CTG996CTT (5400G>T), ATT998GCT (5404A>G 5405T>C), AAT999GAT (5407A>G), AAG1001AAA (5415G>A), AGT1010AGC (5442T>C), GGT1012GGA (5448T>A), GAA1015GAG (5457A>G), AAT1018GAC (5464A>G 5466T>C), TCA1020ATA (5470T>A 5471C>T), ATT1021TTA (5473A>T 5475T>A), ACT1024ACC (5484T>C), TTA1025CTA (5485T>C), ACT1026ACC (5490T>C), TTA1028TTG (5496A>G), ACG1029ACC (5499G>C), CTA1030ATG (5500C>A 5502A>G), GAA1031GAG (5505A>G), TCT1034ACT (5512T>A), AAG1035del (5515_5517delAAG), GAT1036AAT (5518G>A), CTC1039GTC (5527C>G)
Endonuclease/integrase (IN) (NP_955580.1)	200	246	11.3%	259	83.8%	46 (97.9%)	35 (74.5%)	0/1/0/0	0
Protein mutations:	L201I (5395C>A), I204A (5404A>G 5405T>C), N205D (5407A>G), N224D (5464A>G 5466T>C), S226I (5470T>A 5471C>T), I227L (5473A>T 5475T>A), L236M (5500C>A 5502A>G), S240T (5512T>A), K241del (5515_5517delAAG), D242N (5518G>A), L245V (5527C>G)
Codon mutations:	CTA201ATA (5395C>A), CTG202CTT (5400G>T), ATT204GCT (5404A>G 5405T>C), AAT205GAT (5407A>G), AAG207AAA (5415G>A), AGT216AGC (5442T>C), GGT218GGA (5448T>A), GAA221GAG (5457A>G), AAT224GAC (5464A>G 5466T>C), TCA226ATA (5470T>A 5471C>T), ATT227TTA (5473A>T 5475T>A), ACT230ACC (5484T>C), TTA231CTA (5485T>C), ACT232ACC (5490T>C), TTA234TTG (5496A>G), ACG235ACC (5499G>C), CTA236ATG (5500C>A 5502A>G), GAA237GAG (5505A>G), TCT240ACT (5512T>A), AAG241del (5515_5517delAAG), GAT242AAT (5518G>A), CTC245GTC (5527C>G)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43