Genome Detective

NGS Details (SRR3458562_Metagenome_example): Friend murine leukemia virus

Assembly

Coverage Length

280 (2 contig(s))

Depth Of Coverage

2.1

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

Friend murine leukemia virus (Taxonomy ID: 11795)

Reference Genome

NC_001362.1

NT Identity (%)

75.0903

AA Identity (%)

79.5699

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

266.0 (NT) + 511.0 (AA) = 777.0

Concordance (%)

67.7419

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 5233 and ends at position 7583 relative to NC_001362.1 reference sequence.

NC_001362.1

SRR3458562_Metagenome_example-NC_001362.1-72-0

NC_001362.1

SRR3458562_Metagenome_example-NC_001362.1-72-0

NC_001362.1

SRR3458562_Metagenome_example-NC_001362.1-72-0

GCGCCAGTCCTCCGATAGACTGAGTCGCCCGGGTACCCGTGTATCCAATAAATCCTCTTGCTGTTGCATCCGACTCGTGGTCTCGCTGTTCCTTGGGAGGGTCTCCTCAGAGTGATTGACTACCCGTCTCGGGGGTCTTTCATTTGGGGGCTCGTCCGGGATCTGGAGACCCCTGCCCAGGGACCACCGACCCACCACCGGGAGGTAAGCTGGCCAGCAATTGTTCTGTGTCTGTCCATTGTCCTGTGTCTTTGATTGATTTTATGCGCCTGTGTCTGTACTAGTTGGCCGACTAGATTGGTATCTGGCGGATCCGTGGTGGAACTGACGAGTTCGAGACACCCGGCCGCAACCCTGGGAGACGTCCCAGGGACTTCGGGGGCCATTTTTGTGGCCCGGCCAGAGTCCAACCATCCCGATCGTTTTGGACTCTTTGGTGCACCCCCCTTAGAGGAGGGGTATGTGGTTCTGGTAGGAGACAGAGGGCTAAAACGGTTTCCGCCCCCGTCTGAGTTTTTGCTTTCGGTTTGGAACCGAAGCCGCGCCGCGCGTCTTGTCTGCTGCAGCATCGTTCTGTGTTGTCTCTGTTTGACTGTTTTTCTGTATTTGTCTGAAAACATGGGCCAGGCTGTTACCACCCCCTTAAGTTTGACTTTAGACCACTGGAAGGATGTCGAACGGACAGCCCACAACCTGTCGGTAGAGGTTAGAAAAAGGCGCTGGGTTACATTCTGCTCTGCAGAATGGCCAACCTTCAACGTCGGATGGCCACGAGACGGCACTTTTAACCCAGACATTATTACACAGGTTAAGATCAAGGTCTTCTCACCTGGCCCACATGGACATCCGGATCAGGTCCCCTACATCGTGACCTGGGAAGCTATAGCAGTAGACCCCCCTCCCTGGGTCAGACCCTTCGTGCACCCTAAACCTCCCCTCTCTCTTCCCCCTTCAGCCCCCTCTCTCCCACCTGAACCCCCACTCTCGACCCCGCCCCAGT

CCTCCCTCTATCCGGCTCTCACTTCTCCTTTAAACACCAAACCTAGGCCTCAAGTCCTTCCTGATAGCGGAGGACCACTCATTGATCTACTCACGGAGGACCCTCCGCCTTACCGGGACCCAGGGCCACCCTCTCCTGACGGGAACGGCGATAGCGGAGAAGTGGCCCCTACAGAAGGAGCCCCTGACCCTTCCCCAATGGTATCCCGCCTGCGGGGAAGAAAAGAACCCCCCGTGGCGGATTCTACTACCTCTCAGGCGTTCCCCCTTCGCCTGGGAGGGAATGGACAGTATCAATACTGGCCATTTTCCTCCTCTGACCTCTATAACTGGAAAAATAACAACCCCTCTTTCTCCGAGGACCCAGCTAAATTGACAGCTTTGATCGAGTCCGTTCTCCTTACTCATCAGCCCACTTGGGATGACTGCCAACAGCTATTAGGGACCCTGCTGACGGGAGAAGAAAAACAGCGAGTGCTCCTAGAGGCCCGAAAGGCGGTTCGAGGGGAGGACGGACGCCCAACTCAGCTGCCCAATGACATTAATGATGCTTTTCCCTTGGAACGTCCCGACTGGGACTACAACACCCAACGAGGTAGGAACCACCTAGTCCACTATCGCCAGTTGCTCCTAGCGGGTCTCCAAAACGCGGGCAGAAGCCCCACCAATTTGGCCAAGGTAAAAGGGATAACCCAGGGACCTAATGAGTCTCCCTCAGCCTTTTTAGAGAGACTCAAGGAGGCCTATCGCAGATACACTCCTTATGACCCTGAGGACCCAGGGCAAGAAACCAATGTGGCCATGTCATTCATCTGGCAGTCCGCCCCGGATATCGGGCGAAAGTTAGAGCGGTTAGAAGATTTGAAGAGTAAGACCTTAGGAGACTTAGTGAGGGAAGCTGAAAAGATCTTTAATAAACGAGAAACCCCGGAAGAAAGAGAGGAACGTATTAGGAGAGAAACAGAGGAAAAGGAAGAACGCCGTAGGGCAGAGGATGTGCA

GAGAGAGAAGGAGAGGGACCGCAGAAGACATAGAGAAATGAGTAAGTTGCTGGCTACTGTCGTTAGCGGGCAGAGACAGGATAGACAGGGAGGAGAGCGAAGGAGGCCCCAACTCGACCACGACCAGTGTGCCTACTGCAAAGAAAAGGGACATTGGGCTAGAGATTGCCCCAAGAAGCCAAGAGGACCCCGGGGACCACGACCCCAGGCCTCCCTCCTGACCTTAGACGATTAGGGAGGTCAGGGTCAGGAGCCCCCCCCTGAACCCAGGATAACCCTCAGAGTCGGGGGGCAACCCGTCACCTTCCTAGTGGATACTGGGGCCCAACACTCCGTGCTGACCCAAAATCCTGGACCCCTAAGTGACAAGTCTGCCTGGGTCCAAGGGGCTACTGGAGGGAAGCGGTATCGCTGGACCACGGATCGCCGAGTGCACCTAGCCACCGGTAAGGTCACCCATTCTTTCCTCCATGTACCAGATTGCCCCTATCCTCTGCTAGGAAGAGATTTGCTGACTAAACTAAAAGCCCAAATTCACTTTGAGGGATCAGGAGCTCAGGTTGTGGGACCAATGGGACAGCCCCTGCAAGTGCTGACCCTAAACATAGAAGATGAGTATCGGCTACATGAGACCTCAAAAGGGCCAGATGTGCCTCTAGGGTCCACATGGCTCTCTGATTTTCCCCAGGCCTGGGCAGAAACCGGGGGCATGGGGCTGGCCGTTCGCCAAGCTCCTCTGATCATACCTCTGAAGGCAACCTCTACCCCCGTGTCCATAAAACAATACCCCATGTCACAAGAAGCCAGACTGGGGATCAAGCCCCACATACAGAGACTGCTGGATCAGGGAATTCTGGTACCCTGCCAGTCCCCCTGGAACACGCCCCTGCTACCCGTTAAGAAACCGGGGACTAATGATTATAGGCCTGTCCAGGATCTGAGAGAAGTCAACAAGCGGGTGGAAGACATCCACCCCACCGTGCCCAACCCTTACAACCTC

TTGAGCGGGCTCCCACCGTCCCACCAGTGGTACACTGTGCTTGACTTAAAAGATGCTTTTTTCTGCCTGAGACTCCACCCCACCAGTCAGTCTCTCTTCGCCTTTGAGTGGAGAGATCCAGAGATGGGAATCTCAGGACAATTAACCTGGACCAGACTCCCGCAGGGTTTCAAAAACAGTCCCACCCTGTTTGATGAAGCCCTGCACAGGGACCTCGCAGACTTCCGGATCCAGCACCCAGACCTGATTCTGCTCCAGTATGTAGATGACTTACTGCTGGCCGCCACTTCTGAGCTTGACTGTCAACAAGGTACGCGGGCCCTGTTACAAACCCTAGGGGACCTCGGATATCGGGCCTCGGCCAAGAAAGCCCAAATTTGCCAGAAACAGGTCAAGTATCTGGGGTATCTTCTAAAAGAGGGTCAGAGATGGCTGACTGAGGCCAGAAAAGAGACTGTGATGGGGCAGCCTACTCCGAAGACCCCTCGACAACTAAGGGAGTTCCTAGGGACGGCAGGCTTCTGTCGCCTCTGGATCCCTGGGTTTGCAGAAATGGCAGCCCCCTTGTACCCTCTCACCAAAACGGGGACTCTGTTTGAGTGGGGCCCAGACCAGCAAAAGGCCTACCAAGAGATCAAGCAGGCTCTCTTAACTGCCCCTGCCCTGGGATTGCCAGACTTGACTAAGCCCTTCGAACTTTTTGTTGACGAGAAGCAGGGCTACGCCAAAGGTGTCCTAACGCAAAAACTGGGGCCTTGGCGTCGGCCGGTGGCCTACCTGTCCAAAAAGCTAGACCCAGTGGCAGCTGGGTGGCCCCCTTGCCTACGGATGGTAGCAGCCATCGCCGTTCTGACCAAAGACGCTGGCAAGCTCACCATGGGACAGCCACTAGTCATTCTGGCCCCCCATGCAGTAGAGGCACTAGTTAAGCAACCCCCTGATCGCTGGCTCTCCAACGCCCGAATGACCCACTACCAGGCTCTGCTTCTGGACACGGACC

GAGTCCAGTTCGGACCAATAGTGGCCCTAAACCCAGCTACGCTGCTCCCTCTACCTGAGGAGGGGCTGCAACATGACTGCCTTGACATCTTGGCTGAAGCCCACGGAACTAGACCAGATCTTACGGACCAGCCTCTCCCAGACGCTGACCACACCTGGTACACAGATGGGAGCAGCTTCCTGCAAGAGGGGCAGCGCAAGGCCGGAGCAGCAGTAACCACCGAGACCGAGGTAGTCTGGGCCAAAGCACTGCCAGCCGGGACATCGGCCCAAAGAGCTGAGTTGATAGCGCTCACCCAAGCCTTAAAAATGGCAGAAGGTAAGAAGCTGAATGTTTACACCGATAGCCGTTATGCTTTTGCCACTGCCCATATTCACGGAGAAATATATAGAAGGCGCGGGTTGCTCACATCAGAAGGAAAAGAAATCAAAAATAAGGACGAGATCTTGGCCCTACTGAAGGCTCTCTTCCTGCCCAAAAGACTTAGCATAATTCATTGCCCGGGACATCAGAAGGGAAACCGCGCGGAGGCAAGGGGCAACAGGATGGCCGACCAAGCGGCCCGAGAAGTAGCCACTAGAGAAACTCCAGAGACTTCCACACTTCTGATAGAAAATTCAGCCCCCTATACTCATGAACATTTTCACTATACGGTGACTGACATAAAAGATCTGACTAAACTAGGGGCCACTTATGACGATGCAAAGAAGTGTTGGGTTTATCAGGGAAAGCCTGTAATGCCTGATCAATTCACCTTTGAACTATTAGATTTTCTTCATCAATTGACCCACCTCAGTTTCTCAAAAACAAAGGCTCTTCTAGAAAGGAACTACTGTCCTTATTACATGCTGAACCGGGATCGAACGCTCAAAGACATCACTGAGACTTGCCAAGCCTGTGCACAGGTCAATGCCAGCAAGTCTGCCGTCAAACAAGGGACTAGAGTTCGAGGGCACCGACCCGGCACCCACTGGGAAATTGATTTCACTGAGGTAAAACC

TGGCCTGTATGGGTATAAATATCTTTTAGTTTTCATAGACACTTTCTCTGGATGGGTAGAAGCTTTCCCAACCAAGAAAGAAACTGCCAAAGTTGTAACCAAGAAGCTACTAGAAGAAATCTTCCCCAGATTCGGCATGCCACAGGTATTGGGAACCGACAATGGGCCTGCCTTCGTCTCCAAGGTAAGTCAGACAGTAGCCGATTTACTGGGGGTTGATTGGAAACTACATTGTGCTTACAGACCCCAGAGTTCAGGTCAGGTAGAAAGAATGAATAGGACAATCAAGGAGACTTTAACTAAATTGACGCTTGCAACTGGCTCTAGGGACTGGGTGCTCCTGCTTCCCCTAGCCCTGTATCGAGCCCGCAACACGCCGGGCCCCCATGGTCTCACCCCATATGAAATCTTATATGGGGCACCCCCGCCCCTTGTAAACTTCCCTGATCCTGACATGGCAAAGGTTACTCATAACCCCTCTCTCCAAGCCCATTTACAGGCACTCTACCTGGTCCAGCACGAAGTCTGGAGACCGTTGGCGGCAGCTTACCAAGAACAACTGGACCGGCCGGTAGTGCCTCACCCTTTCCGAGTCGGTGACACAGTGTGGGTCCGCAGACACCAAACTAAAAATCTAGAACCCCGCTGGAAAGGACCTTATACCGTCCTACTGACTACCCCCACCGCTCTCAAAGTGGACGGCATTGCAGCGTGGATCCACGCTGCCCACGTAAAGGCTGCCGACACCAGGATTGAGCCACCATCGGAATCGACATGGCGTGTTCAACGCTCTCAAAATCCCCTAAAGATAAGATTGACCCGCGGGACCTCCTAATCCCCTTAATTCTCTTCCTGTCTCTCAAAGGGGCCAGATCCGCAGCACCCGGCTCCAGCCCTCACCAGGTCTACAACATTACCTGGGAAGTGACCAATGGGGATCGGGAGACAGTATGGGCAATATCAGGCAACCACCCTCTGTGGACTTGGTGGCCAGTCCTCA

CCCCAGATTTGTGTATGTTAGCTCTCAGTGGGCCGCCCCACTGGGGGCTAGAGTATCAGGCCCCCTATTCCTCGCCCCCGGGGCCCCCTTGTTGCTCAGGGAGCAGCGGGAACGTTGCAGGCTGTGCCAGAGACTGCAACGAGCCCTTGACCTCCCTCACCCCTCGGTGCAACACTGCCTGGAACAGACTTAAGCTGGACCAGGTAACTCATAAATCAAGTGAGGGATTTTATGTCTGCCCCGGGTCACATCGCCCCCGGGAAGCCAAGTCCTGTGGGGGTCCAGACTCCTTCTACTGTGCCTCTTGGGGCTGCGAGACAACCGGTAGAGTATACTGGAAGCCCTCCTCTTCTTGGGACTACATCACAGTAGACAACAATCTCACCTCTAACCAGGCTGTTCAGGTATGCAAAGACAATAAGTGGTGCAATCCCTTGGCTATCCGGTTTACAAACGCCGGGAAACAGGTCACCTCATGGACAACTGGACACTATTGGGGTCTACGTCTTTATGTCTCTGGACAGGACCCAGGGCTTACTTTCGGGATCCGACTCAGTTATCAAAATCTAGGACCTCGGATCCCAATAGGACCAAACCCCGTCCTGGCAGACCAACTTTCGTTCCCGCTACCTAATCCCCTACCCAAACCTGCCAAGTCTCCCCCCGCCTCTAGTTCGACTCCCACATTGATTTCCCCGTCCCCCACTCCCACTCAGCCCCCGCCAGCAGGAACGGGAGACAGATTACTAAATCTAGTACAGGGAGCTTACCAGGCACTCAACCTTACCAACCCTGATAAAACTCAAGAGTGCTGGTTATGCCTAGTGTCTGGACCCCCCTATTACGAGGGGGTTGCCGTCCTAGGTACTTATTCCAACCATACCTCTGCCCCAGCTAACTGCTCCGTGGCCTCCCAACACAAGCTGACCCTGTCCGAAGTGACTGGACGGGGACTCTGCATAGGAACAGTCCCAAAAACTCACCAGGCCCTGTGCAACAC

TACCCTTAAGGCAGGCAAAGGGTCTTACTATCTAGTTGCCCCCACAGGAACTATGTGGGCATGTAACACTGGACTCACTCCATGCCTATCTGCCACCGTGCTTAATCGCACCACTGACTATTGCGTTCTCGTGGAATTATGGCCCAGGGTCACCTACCATCCTCCCAGTTACGTCTATAGCCAGTTTGAAAAATCCCATAGACATAAAAGAGAACCAGTGTCCTTAACCTTGGCCTTATTATTAGGTGGGCTAACTATGGGTGGCATCGCCGCGGGAGTAGGGACAGGAACTACCGCCCTGGTCGCCACCCAGCAGTTTCAGCAGCTCCATGCTGCCGTACAAGATGATCTCAAAGAAGTCGAAAAGTCAATTACTAACCTAGAAAAGTCTCTTACTTCGTTGTCTGAGGTTGTACTGCAGAATCGACGAGGCCTAGACCTGTTGTTCCTAAAAGAGGGAGGACTGTGTGCTGCCCTAAAAGAAGAATGTTGTTTCTATGCTGACCATACAGGCCTAGTAAGAGATAGTATGGCCAAATTAAGAGAGAGACTCTCTCAGAGACAAAAACTATTTGAGTCGAGCCAAGGATGGTTCGAAGGATGGTTTAACAGATCCCCCTGGTTTACCACGTTGATATCCACCATCATGGGGCCTCTCATTATACTCCTACTAATTCTGCTTTTTGGACCCTGCATTCTTAATCGATTAGTTCAATTTGTTAAAGACAGGATCTCAGTAGTCCAGGCTTTAGTCCTGACTCAACAATACCACCAGCTAAAACCACTAGAATACGAGCCACAATAAATAAAAGATTTTATTTAGTTTCCAGAAAAAGGGGGGAATGAAAGACCCCACCAAATTGCTTAGCCTGATAGCCGCAGTAACGCCATTTTGCAAGGCATGGAAAAATACCAAACCAAGAATAGAGAAGTTCAGATCAAGGGCGGGTACACGAAAACAGCTAACGTTGGGCCAAACAGGATATCTGCGGTGAGCAGT

TTCGGCCCCGGCCCGGGGCCAAGAACAGATGGTCACCGCGGTTCGGCCCCGGCCCGGGGCCAAGAACAGATGGTCCCCAGATATGGCCCAACCCTCAGCAGTTTCTTAAGACCCATCAGATGTTTCCAGGCTCCCCCAAGGACCTGAAATGACCCTGTGCCTTATTTGAATTAACCAATCAGCCTGCTTCTCGCTTCTGTTCGCGCGCTTCTGCTTCCCGAGCTCTATAAAAGAGCTCACAACCCCTCACTCGGCGCGCCAGTCCTCCGATAGACTGAGTCGCCCGGGTACCCGTGTATCCAATAAATCCTCTTGCTGTTGCA

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

........................................................................................................................................................................................................................................TGCGCTTACAGGCCCCAGAGTTCAGGACAGGTAGAGAGGATGAATCGGACCTTAAAAGAGACCTTAACTAAATTGACTATGGAGACTGGCGCT---AATTGGGTGGTCCTTCTCCCCTACGCTCTGTTCGGGGCCCGTAACACCC...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

................................................................................................................................................................................................................................................................................................................................................................................................................................................................CTAAAGGAAGGCGGGCTCTGTGCAGCCCTCAAAGAACAATGTTGCTTTTACGCAGACCATTCAGGAGTGGTTAAAGATTCTATGGCAAAACTAAGAGAAAGATTAGACAAACGAAAAAAAGAAAGAGAGTCGAGC.................................................................................................................................................................................................................................................................................................................................................................................................................................

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gag

MGQAVTTPLSLTLDHWKDVERTAHNLSVEVRKRRWVTFCSAEWPTFNVGWPRDGTFNPDIITQVKIKVFSPGPHGHPDQVPYIVTWEAIAVDPPPWVRPFVHPKPPLSLPPSAPSLPPEPPLSTPPQSSLYPALTSPLNTKPRPQVLPDSGGPLIDLLTEDPPPYRDPGPPSPDGNGDSGEVAPTEGAPDPSPMVSRLRGRKEPPVADSTTSQAFPLRLGGNGQYQYWPFSSSDLYNWKNNNPSFSEDPAKLTALIESVLLTHQPTWDDCQQLLGTLLTGEEKQRVLLEARKAVRGEDGRPTQLPNDINDAFPLERPDWDYNTQRGRNHLVHYRQLLLAGLQNAGRSPTNLAKVKGITQGPNESPSAFLERLKEAYRRYTPYDPEDPGQETNVAMSFIWQSAPDIGRKLERLEDLKSKTLGDLVREAEKIFNKRETPEEREERIRRETEEKEERRRAEDVQREKERDRRRHREMSKLLATVVSGQRQDRQGGERRRPQLDHDQCAYCKEKGHWARDCPKKPRGPRGPRPQASLLTLDD*

pol

TLDD*GGQGQEPPPEPRITLRVGGQPVTFLVDTGAQHSVLTQNPGPLSDKSAWVQGATGGKRYRWTTDRRVHLATGKVTHSFLHVPDCPYPLLGRDLLTKLKAQIHFEGSGAQVVGPMGQPLQVLTLNIEDEYRLHETSKGPDVPLGSTWLSDFPQAWAETGGMGLAVRQAPLIIPLKATSTPVSIKQYPMSQEARLGIKPHIQRLLDQGILVPCQSPWNTPLLPVKKPGTNDYRPVQDLREVNKRVEDIHPTVPNPYNLLSGLPPSHQWYTVLDLKDAFFCLRLHPTSQSLFAFEWRDPEMGISGQLTWTRLPQGFKNSPTLFDEALHRDLADFRIQHPDLILLQYVDDLLLAATSELDCQQGTRALLQTLGDLGYRASAKKAQICQKQVKYLGYLLKEGQRWLTEARKETVMGQPTPKTPRQLREFLGTAGFCRLWIPGFAEMAAPLYPLTKTGTLFEWGPDQQKAYQEIKQALLTAPALGLPDLTKPFELFVDEKQGYAKGVLTQKLGPWRRPVAYLSKKLDPVAAGWPPCLRMVAAIAVLTKDAGKLTMGQPLVILAPHAVEALVKQPPDRWLSNARMTHYQALLLDTDRVQFGPIVALNPATLLPLPEEGLQHDCLDILAEAHGTRPDLTDQPLPDADHTWYTDGSSFLQEGQRKAGAAVTTETEVVWAKALPAGTSAQRAELIALTQALKMAEGKKLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIHCPGHQKGNRAEARGNRMADQAAREVATRETPETSTLLIENSAPYTHEHFHYTVTDIKDLTKLGATYDDAKKCWVYQGKPVMPDQFTFELLDFLHQLTHLSFSKTKALLERNYCPYYMLNRDRTLKDITETCQACAQVNASKSAVKQGTRVRGHRPGTHWEIDFTEVKPGLYGYKYLLVFIDTFSGWVEAFPTKKETAKVVTKKLLEEIFPRFGMPQVLGTDNGPAFVSKVSQTVADLLGVD

WKLHCAYRPQSSGQVERMNRTIKETLTKLTLATGSRDWVLLLPLALYRARNTPGPHGLTPYEILYGAPPPLVNFPDPDMAKVTHNPSLQAHLQALYLVQHEVWRPLAAAYQEQLDRPVVPHPFRVGDTVWVRRHQTKNLEPRWKGPYTVLLTTPTALKVDGIAAWIHAAHVKAADTRIEPPSESTWRVQRSQNPLKIRLTRGTS*

....CAYRPQSSGQVERMNRTLKETLTKLTMETGA-NWVVLLPYALFGARNTX........................................................................................................................................................

env

MACSTLSKSPKDKIDPRDLLIPLILFLSLKGARSAAPGSSPHQVYNITWEVTNGDRETVWAISGNHPLWTWWPVLTPDLCMLALSGPPHWGLEYQAPYSSPPGPPCCSGSSGNVAGCARDCNEPLTSLTPRCNTAWNRLKLDQVTHKSSEGFYVCPGSHRPREAKSCGGPDSFYCASWGCETTGRVYWKPSSSWDYITVDNNLTSNQAVQVCKDNKWCNPLAIRFTNAGKQVTSWTTGHYWGLRLYVSGQDPGLTFGIRLSYQNLGPRIPIGPNPVLADQLSFPLPNPLPKPAKSPPASSSTPTLISPSPTPTQPPPAGTGDRLLNLVQGAYQALNLTNPDKTQECWLCLVSGPPYYEGVAVLGTYSNHTSAPANCSVASQHKLTLSEVTGRGLCIGTVPKTHQALCNTTLKAGKGSYYLVAPTGTMWACNTGLTPCLSATVLNRTTDYCVLVELWPRVTYHPPSYVYSQFEKSHRHKREPVSLTLALLLGGLTMGGIAAGVGTGTTALVATQQFQQLHAAVQDDLKEVEKSITNLEKSLTSLSEVVLQNRRGLDLLFLKEGGLCAALKEECCFYADHTGLVRDSMAKLRERLSQRQKLFESSQGWFEGWFNRSPWFTTLISTIMGPLIILLLILLFGPCILNRLVQFVKDRISVVQALVLTQQYHQLKPLEYEPQ*

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	5233	7583	3.4%	266	49.1%	277 (98.9%)	208 (74.3%)	0/3
Mutations:	5235T>C 5244A>G 5259T>A 5268A>G 5271A>G 5278A>C 5283A>C 5284A>T 5286C>A 5289G>A 5295T>C 5310G>T 5311C>A 5313T>G 5315C>A 5316A>G 5323T>G 5326_5328delAGG 5329G>A 5331C>T 5338C>G 5343G>T 5346T>C 5350C>T 5351T>A 5352A>C 5355C>T 5360A>T 5361T>C 5362C>G 5364A>G 5370C>T 5376G>C 7454A>G 7457G>A 7460A>C 7463A>G 7466G>C 7472T>A 7478A>C 7485G>C 7493T>C 7496C>T 7499T>C 7502T>A 7509A>T 7514C>A 7515C>G 7517A>G 7520A>T 7522G>A 7527A>T 7528G>C 7535C>A 7539T>C 7547G>A 7551C>T 7553C>A 7554T>G 7555C>A 7556T>C 7557C>A 7559G>A 7560A>C 7563C>A 7569C>G 7570T>A 7572T>A 7573T>G 7574T>A
CDS

pol	1005	1053	4.1%	258	83.0%	48 (98.0%)	38 (77.6%)	0/1/0/0	0
Protein mutations:	I1022L (5284A>T 5286C>A) L1031M (5311C>A 5313T>G) A1032E (5315C>A 5316A>G) S1035A (5323T>G) R1036del (5326_5328delAGG) D1037N (5329G>A 5331C>T) L1040V (5338C>G) L1044Y (5350C>T 5351T>A 5352A>C) Y1047F (5360A>T 5361T>C) R1048G (5362C>G 5364A>G)
Codon mutations:	TGT1005TGC (5235T>C) AGA1008AGG (5244A>G) GGT1013GGA (5259T>A) GAA1016GAG (5268A>G) AGA1017AGG (5271A>G) AGG1020CGG (5278A>C) ACA1021ACC (5283A>C) ATC1022TTA (5284A>T 5286C>A) AAG1023AAA (5289G>A) ACT1025ACC (5295T>C) ACG1030ACT (5310G>T) CTT1031ATG (5311C>A 5313T>G) GCA1032GAG (5315C>A 5316A>G) TCT1035GCT (5323T>G) AGG1036del (5326_5328delAGG) GAC1037AAT (5329G>A 5331C>T) CTC1040GTC (5338C>G) CTG1041CTT (5343G>T) CTT1042CTC (5346T>C) CTA1044TAC (5350C>T 5351T>A 5352A>C) GCC1045GCT (5355C>T) TAT1047TTC (5360A>T 5361T>C) CGA1048GGG (5362C>G 5364A>G) CGC1050CGT (5370C>T) ACG1052ACC (5376G>C)
env	559	603	6.6%	253	82.7%	45 (100%)	36 (80.0%)	0/0/0/0	0
Protein mutations:	E571Q (7485G>C) T579S (7509A>T) L581V (7515C>G 7517A>G) R583K (7522G>A) S594D (7554T>G 7555C>A 7556T>C) Q595K (7557C>A 7559G>A) Q597K (7563C>A) L599E (7569C>G 7570T>A) F600R (7572T>A 7573T>G 7574T>A)
Codon mutations:	AAA560AAG (7454A>G) GAG561GAA (7457G>A) GGA562GGC (7460A>C) GGA563GGG (7463A>G) CTG564CTC (7466G>C) GCT566GCA (7472T>A) CTA568CTC (7478A>C) GAA571CAA (7485G>C) TGT573TGC (7493T>C) TTC574TTT (7496C>T) TAT575TAC (7499T>C) GCT576GCA (7502T>A) ACA579TCA (7509A>T) GGC580GGA (7514C>A) CTA581GTG (7515C>G 7517A>G) GTA582GTT (7520A>T) AGA583AAA (7522G>A) AGT585TCT (7527A>T 7528G>C) GCC587GCA (7535C>A) TTA589CTA (7539T>C) GAG591GAA (7547G>A) CTC593TTA (7551C>T 7553C>A) TCT594GAC (7554T>G 7555C>A 7556T>C) CAG595AAA (7557C>A 7559G>A) AGA596CGA (7560A>C) CAA597AAA (7563C>A) CTA599GAA (7569C>G 7570T>A) TTT600AGA (7572T>A 7573T>G 7574T>A)
Proteins

RNA-dependent DNA polymerase (NP_040333.1)	1005	1053	4.1%	258	83.0%	48 (98.0%)	38 (77.6%)	0/1/0/0	0
Protein mutations:	I1022L (5284A>T 5286C>A) L1031M (5311C>A 5313T>G) A1032E (5315C>A 5316A>G) S1035A (5323T>G) R1036del (5326_5328delAGG) D1037N (5329G>A 5331C>T) L1040V (5338C>G) L1044Y (5350C>T 5351T>A 5352A>C) Y1047F (5360A>T 5361T>C) R1048G (5362C>G 5364A>G)
Codon mutations:	TGT1005TGC (5235T>C) AGA1008AGG (5244A>G) GGT1013GGA (5259T>A) GAA1016GAG (5268A>G) AGA1017AGG (5271A>G) AGG1020CGG (5278A>C) ACA1021ACC (5283A>C) ATC1022TTA (5284A>T 5286C>A) AAG1023AAA (5289G>A) ACT1025ACC (5295T>C) ACG1030ACT (5310G>T) CTT1031ATG (5311C>A 5313T>G) GCA1032GAG (5315C>A 5316A>G) TCT1035GCT (5323T>G) AGG1036del (5326_5328delAGG) GAC1037AAT (5329G>A 5331C>T) CTC1040GTC (5338C>G) CTG1041CTT (5343G>T) CTT1042CTC (5346T>C) CTA1044TAC (5350C>T 5351T>A 5352A>C) GCC1045GCT (5355C>T) TAT1047TTC (5360A>T 5361T>C) CGA1048GGG (5362C>G 5364A>G) CGC1050CGT (5370C>T) ACG1052ACC (5376G>C)
envelope protein (NP_040334.1)	559	603	6.6%	253	82.7%	45 (100%)	36 (80.0%)	0/0/0/0	0
Protein mutations:	E571Q (7485G>C) T579S (7509A>T) L581V (7515C>G 7517A>G) R583K (7522G>A) S594D (7554T>G 7555C>A 7556T>C) Q595K (7557C>A 7559G>A) Q597K (7563C>A) L599E (7569C>G 7570T>A) F600R (7572T>A 7573T>G 7574T>A)
Codon mutations:	AAA560AAG (7454A>G) GAG561GAA (7457G>A) GGA562GGC (7460A>C) GGA563GGG (7463A>G) CTG564CTC (7466G>C) GCT566GCA (7472T>A) CTA568CTC (7478A>C) GAA571CAA (7485G>C) TGT573TGC (7493T>C) TTC574TTT (7496C>T) TAT575TAC (7499T>C) GCT576GCA (7502T>A) ACA579TCA (7509A>T) GGC580GGA (7514C>A) CTA581GTG (7515C>G 7517A>G) GTA582GTT (7520A>T) AGA583AAA (7522G>A) AGT585TCT (7527A>T 7528G>C) GCC587GCA (7535C>A) TTA589CTA (7539T>C) GAG591GAA (7547G>A) CTC593TTA (7551C>T 7553C>A) TCT594GAC (7554T>G 7555C>A 7556T>C) CAG595AAA (7557C>A 7559G>A) AGA596CGA (7560A>C) CAA597AAA (7563C>A) CTA599GAA (7569C>G 7570T>A) TTT600AGA (7572T>A 7573T>G 7574T>A)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43