Genome Detective

NGS Details (SRR3458562_Metagenome_example): Pinniped bocaparvovirus 2

Assembly

Coverage Length

1030 (6 contig(s))

Depth Of Coverage

1.0

Number Of Reads

Reads Per Million

0.65 rpm (after QC)

Ambiguities

Assembly Method

de novo + reference guided assembly

Consensus Caller

Bcf Tools

Coverage Map

Map

Variant Tables

Consensus Variants

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Minority Variants

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SNP Variants Table

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Annotated Variants Table

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Assignment

Type

Pinniped bocaparvovirus 2 (Taxonomy ID: 1511870)

Reference Genome

NC_038536.1

NT Identity (%)

93.8735

AA Identity (%)

91.222

Number Of Stop Codons

Number Of CDS

Alignment

Alignment Score

1746.0 (NT) + 3405.0 (AA) = 5151.0

Concordance (%)

88.7033

Alignment Method

Global, seeded, nucleotide + amino acids (AGA)

NT Alignment

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Region Bam File

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CDS Alignment

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Consensus Sequence

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Consensus Contigs

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Genome Region

Sequence starts at position 453 and ends at position 4706 relative to NC_038536.1 reference sequence.

NC_038536.1

SRR3458562_Metagenome_example-NC_038536.1-120-0

NC_038536.1

SRR3458562_Metagenome_example-NC_038536.1-120-0

NC_038536.1

SRR3458562_Metagenome_example-NC_038536.1-120-0

GCGCTGTTAATGTTCCTGCGGCCAATGACGTATACAACAACATATGCATATAAAGATTATATCAAAAGCGAAAGCATTCATGTAATGAGTAACCTATAAAGGTCATAGTCCGTGTTAATGAATAACCAGACAGCCAATCAGGAAAGAGCACGCCCATGGTGTGATGGGCGGAGAGGGGCGTTACTGGGCGGGGAAATGAGTATATAAGCACGCGCACATCCGGGTTCAAGTCATTCTGCTTCCGGGATCCGTCGGAGACAGACCTCTCTCGGTGAGTGATGGCGATTCCTCTTGCTGCTGTCAATGATCTTATGCAATTTCCTGGGCCTTGCTATACCTATGTGCTCAAATTTCCATACGCTGACTGGCGCTTCAATGAGATCCGTCTACAACGGGCACTGGGATATCCAACTCATGACATCCTGGATAATCCCGACATCTATGCGTCTATGCCGGGTCAGTCTGAGCCTGCTGAACAATCTGCATTCCTTGAGACCAGAGGACCAATGCAGGCATACACCCTATTACTGGCACGCACTGCTTATACGGCGGCATTTAGCTTTTTCTCGGCGAAGCAAGGGAAATGCCCTCCTGCTGCTAGTATTTTTACTCAATGTGAACTTGGCGAGCGAGATCTTCATGTACATGTAGTGATGGGTGGAGAAGGCCTGTCAAGATACAACGCCAAAGCCATCCGGTCTCAATTAGCCTTCAAGTGGCTAGACGCCATTCAGAGTCAGCTTGAATACAATTTGAAGTACGGGCACACGGCTGACAAGGTCTTTTGTGATGTTCTGATTGATTGCTGCTACCGCGCCAAGCAAACATGTGTAGACATGAAAACCCAATACTGTGATGTGCTTCAATACAAGAGCCGAAGCGGCGAGATGTATGCCTGCCGAGTAGATGCGCTAGACTACATCTGTAACTATCTTCTCTGCAAGAATCTCCGCTTCTTTACACATGTTGATCCAGAAAAGGCGACTCCGTTTGTCGCCTA

CTTTCCGTGCACCAATAAGACGTATGCCGCATCATTTGTGAATGGGAAGTGGATTCCGATTGAGCTTAGAAAACAATGGCTTCAGTATCTCAGAGACTCTGTAGTTAAAAAGCTTGAGCCGGTATTCTCTGGTGATATATTCGGAGATCTTCCAAAGGTACCTAATGCCAAATGGCAGACTGATTCTGCTTCTCCATCATCAAGCAAGCCAACAAAAAGAGAGACTTTAATGCTTGATTGTATTGATCGCTGTGAAAAGAATCACTATCTCACATATGAAGATCTTGTTGATGGCTGTCCTGATCTTGTAATCATGCTAGAATCACAACCCGGGGGGAGTCGCTTGATTGAGACATTGATTCAGATGGTTCACATAAAGCTATGTCAAAAATATACTGCTTTGAGCTATATTCGAATGAGATATGAGCCTATTGAATTGATTCCATCAAACAAGGCATATCAGCTACTGGCCTTTCAGGGATACAATCCCTTTCAAGCATTTCACTGGCTTTGCTGTGTTTTAAATAAAACAGCCGGCAAACAAAACACAGTTAGTTTCTTTGGGCCAGCTAGCACTGGAAAAACCAACATGGCTAAATCCATAGTTAACGCTGCCAAGCTATATGGATGTGTTAATCACCAAAACAAGAATTTTGTGTTCAATGATTGTGCCTCTAAATTTGTATGTTGGTGGGAAGAGTGCTTGATGCATTCTGACTGGGTTGAGCAGGCTAAATGTATCCTTGGCGGTACTGAATTTAGAATTGACAGAAAACATAGAGATTCCATGCTCCTTCCACAAACGCCTTTAATTATTTCTACCAACAATGACATTTACACGGTTGTTGGTGGAAATACTGTATCCCATGTACATGCAAAGCCTTTAAAGGAACGAGTTGTTCAGCTCAACTTTATGAAACAGCTACAACCGACATTCGGGGAAATCACTCCTGAAGACGTGATTGCTCTTCTACAAGCCTGTATCGATCGCTTTCCTGAT

TTGACTCTGGCTGGCTTCTGCGCTCAGTGGAACCTAGAGAAGGTTCCCAATGATTTTCCTCTCGCTAATCTCTGTCCTGGTCATGTTCAGGACTTTGTTCTGTATGAGCACGGGCTGTGCACTGCATGTGGAGGCTACTATCCGCTAGAGGAGAGAGACCGTGGTGACGTGGAAGCTGCTGTGACAGCAGAACCTGCGCCTGCTGAGTTCAAAGTACCAGGTAAGCTATTACTCATATGGGTGTTGCCTTTCCGCGTTGTTTCTGCTGACACTGACACTGATTCATTTATTACAGCTACTCCGCCTAACACGCCAACCAAGAGGCGTCGGGCAGAGTCCACTGACAGTGGACCTTCAACTTCCACGCAGTCTTCTCCTGCGAAAAAGCCTCGCAAGCAAAAGGTGAGAACCAAGATCCTCTTTGAGGACGATTGGTCTGCTCAGCCTAGTGATCGCCTAGACAGAATTCGCTATGAGCGGTTCGTCAAAAGCATCACACGCTCGCCGCGAGCAGAGGACGAGGAGTCGGAGCCGGAGTCGGAGTCCTCCGAGATGTCGCCGGCAGAATGGGGGGAGATGCTCGGCCTCATCACGCGGGGACTGGAGGACGAACCGATCGTCCTCCACTGCTTCGAGACGCTTGAAGGGCTCGAAGACGACACCGATGGAAGTCTTCAATCGCCATAAGGCAGAGACTGGCATCAATCTGTCCATGTGTGGCTTCTACTGGCACAGCACTAGACTGGCCAGGGCCGGGACTGATTGGATCTTTAATGAGGGGAAACCATTGTTTCAATCTAAATGTACCAATAATCTTGTATCTTGGGATATTGTAAGAGAAATGTTGTTTCAATTCAAAAAAACAATGGATCAAAAATATAGAAATATATTGTATCATGGGATGAGGGGGGCTGATTGTGATAAATGCAAATACTGGGATAATGTGTACTTGGAACACTTGGCTAACATTGAAACAAATGATGTTGTTATGCAGGACATT

TCTGATGAAGAAATGTTGAGTGCTGCCATGGAGGTAGATGGCACCCACGAATAGAAAGCCTGGTGGCTGGGTGGTGCCTGGATTCAAATACCTGGGACCGTTTAATCCATTAAATAACGGGGAACCTGTAAATTTTGTTGACGCCGCTGCTAAGGCGCATGATCAAGCCTATCAAGATATTATTGATTCTGGTCAAAATCCTTACTTTAGCTTCAATAAAGCTGACGCTGATTTTATTGAGACTCTGTCTCACGACTCTTCTGTTGGTAGTTGGCTGGGCCGCTCTGCGTTCCATCTAAAAAAGGTACTTGCTCCACACTTGCCTCAGGACGGTGGAGAACAGCCGGGGCCTTCAGGGGCAAAGAAGCCGCGCCTTGATCCAAAGCAGGATCGAGCTCAAAAGCGGAAGCTTTACTTTGCTCGCTCCAACAAACAAGCCAAGCAACCGAGAATGTCTGCAGGCGCAGAACCTACAGAAGACGTGGCCGGATCTGCGGATCCCGCGGCCGAGGGAAGGGCGGGAGGAGCCAATGGAGGTGGTGGAGGCATGGGAGGAGGTGGAGGACATGGAGTGGGAGTAAGCACGGGCGGGTGGCAGGCGGGAACTGTGTTTACTGATAGTGCCATTATCACCACGGGAACACGTCAGTGGTACGCGCCCATTTACAATGGTCATTTGTACAAACTGCTGAAACCAGATTCTGGCCTTCATAGCAATTGGACTGGTATCAGCACACCATGGGGATATTTCAATTTCAATGAGTATGACGCGCACTTTTCTCCACAAGACTGGCAGCGTTTGCTGAACGAATATAAACGCTGGCGTCCAAAGTCCATGCATGTGAAGATCTACAACTTGCAAATTAAGCAAGTGGTCACATTGGGTGCGGACACGTTGTATAATAATGATTTGACTGCTGGTGTGCATATATTCTGTGATGGGTCGCATCAGTTCCCATATTCTCAACATCCATGGGATACTGGTGTTATGCCTGAACTT

CCAAATAAGGTATGGAAGCTATCACAGTATGCCTATTTCCAGGCGCTAAATGATCTTATAGATACAAACGCAGGCAGCAACGCAGATGTTGGAAACATTGAAAAACATATAATGAAAGCTGCGCCGTTTTACATTCTGGAAAGCGCTAGTCATCAAGTACTTCGAACCGGAGAAGAAACCAGTTTTACATTTGAATTTGACTGTGGGTGGGTTACCAATGATAGAGTGTATTGTCCACCACAGGCAGATTTTAATCCTTTAGTAAACACGCGCCGATATTTTCCCACAAGACAAACTGGAGCGGGCGCCGCAAACAAATTTACATACCATAGATACAATCCATATAACAAACCGAGCATCTGGATGCCTGGTCCTAGCTTGGGATACATTGGAGCCACTCAAACATCTGCAAATCCAGAAAAAGCACGAGGACCTGTCACTGTTGTCTATCAGCCACCGTATACAACTGCAGACGGAGCCAGCGCAAACACTGAACAAAACAAGGACCAGCAAACACTGCTACCAAAATTGACTGAAGCGTCTATGCAAAATGCTGGATTTGACGTGGCGCCTGTTAACAACGCATGCAATGATCTTGGATACATCACTATGGCATACGATTCCAGGGAAGAAAGTGAGCAAAGTACAACAATCACAGTCAAAGACGTGGACGCGGATTTTGCTAGATATGGGGCTGTGTTTGTACAAGACGGAACAAACAAGGAAATCAAAGCAGACGGAACTGCGCTCACTACACAAGACAGAAAAAACTTTTCAGAACTTAGAAATGTATGGATGTATCCAAATCAGGCATGGGACGCAACTCCCATATCGAGAGATACTCCGATATGGGTAAAGTCGCCAAGAACAGATAGGCACACCATGTTTGATACCTCAGACGGAACGATTCCAATGGCACATCCACCGGGGACCATTTTTGTAAAGGTGGCAAAAATACCAATCCCAGGCGACCAAGACTCATATCTGAATCTATATGTGA

CAGGACAGGTCACTTGCCAAGTCATCTGGGAGGCAGAAAGATTCCAGACCAAAAACTGGAGACCAGAAGTACGAACCGACGTGTCGGCGTTTTCAGACCCCACATTATACACTGTCAATGCGGCGGGGGTATACAATACACCAGAAACATTCAAGGAGGGGATGCCAACAAAGCGCGGGATCAATCGTGTACTGTAACATGGATGTATGTATATACAAGAACGAGACAATAAAGCTTTACATTTTGATATATCTTTATACAGCACCTGTTGTTCACGTCATCATATGTTAATTTTATCATGGCGCGGCTTCTTTGCCCCTGAAGGCCCCGGCTGTTCTCCACCGTCCTGAGGCAAAGAAGCCGCGCCTTGATCCAAAGCAGGATCGAGCTCAAAAGCGGAAGCTTTACTTGCTCGCTCCAACAAACAAGCCAAGCCAAC

....................................................................................................................................................................................................................................................................................................................................................................................................................................................................CCGGGTCAGTCTGAGCCTGCTGAACAATCTGCATTCCTTGAGACCAGAGGACCAATGCAGGCATACACCCTAATACTGGCACGCACTGCTTATACGGCGCCATTTAGCTTTTTCT...................................................................................GTGATGGGTGGAGAAGGCCTGTCAAGGTACAACGCCAAAGCCATCCGGTCTCAATTAGCCTTCAAGTGGCTAG.....................................................................................................................................................................................................................................................................................

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

..................AGACCGGCCATCGAGGTAGATCGCAGCCACGAATAGAAAGCCTGGTGGCTGGGTGGTGCCTGGATTCAAGTACCTGGGACCGTTTAATCCATTAAGTAACGGGGAACCTGTAAATTTTGTTG..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................TGGACTGGTATCAGCACACCATGGGGATATTTCAATTTCAATGAGTATGACGCGCACTTTTCTCCACAAGACTGGCAGCGTTTGCTGAACGAATATAAACGCTGGCGTCCAAAGTCCATGCATGTGAAGATCTACAACTTGCAAATTAAGCAAGTGGTCACATTGGGTGCGGACACGTTGTAT----------AAACTGCTGGTGTGCATATATTCTGTGATGGGTGGGATCAGTTGTCATATTCTGAACATCCATGGGATAGGGGGGCTATGACTGAGCTT

CCATATAAGGTATGGAAGCTAT........................................................................................................TTTTACATTCTGGAAAGCGCTAGTCATCAAGTACTTCGAACCGGAGAAGAAACCAGTTTTACTTTTGAATTTGACTGTGGGTGGGTTACCAATGACAGAGTATATTGTCCACCG--------TTTTAATCCTTTAGTAAACACGCGTCGATATTTTCCTACAAGACAAACGGGGACTGGTGCAAACAATAAATTWACATAYKACAGATACAATCCATACAACAAACCAAGCATCTGGATGCCTGGTCCTAGCCCAGGCTACATTGGAAGCACACAGACAT....................................................................................................................................................................CATGTTAACAACGCTTGCAATGATCTTGGATACATCACTATGGCATACGATTCCAGAGAGGAAAGTGAGCAAAGTACAACAATCACAGTCAAAGACGTAGACGCCGACTTTGCTAGATATGGGGCTGTGTTTGTAC......................................................................................................................................................................................................................................................................................................

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D1R54_gp1

MAIPLAAVNDLMQFPGPCYTYVLKFPYADWRFNEIRLQRALGYPTHDILDNPDIYASMPGQSEPAEQSAFLETRGPMQAYTLLLARTAYTAAFSFFSAKQGKCPPAASIFTQCELGERDLHVHVVMGGEGLSRYNAKAIRSQLAFKWLDAIQSQLEYNLKYGHTADKVFCDVLIDCCYRAKQTCVDMKTQYCDVLQYKSRSGEMYACRVDALDYICNYLLCKNLRFFTHVDPEKATPFVAYFPCTNKTYAASFVNGKWIPIELRKQWLQYLRDSVVKKLEPVFSGDIFGDLPKVPNAKWQTDSASPSSSKPTKRETLMLDCIDRCEKNHYLTYEDLVDGCPDLVIMLESQPGGSRLIETLIQMVHIKLCQKYTALSYIRMRYEPIELIPSNKAYQLLAFQGYNPFQAFHWLCCVLNKTAGKQNTVSFFGPASTGKTNMAKSIVNAAKLYGCVNHQNKNFVFNDCASKFVCWWEECLMHSDWVEQAKCILGGTEFRIDRKHRDSMLLPQTPLIISTNNDIYTVVGGNTVSHVHAKPLKERVVQLNFMKQLQPTFGEITPEDVIALLQACIDRFPDLTLAGFCAQWNLEKVPNDFPLANLCPGHVQDFVLYEHGLCTACGGYYPLEERDRGDVEAAVTAEPAPAEFKVPGKLLLIWVLPFRVVSADTDTDSFITATPPNTPTKRRRAESTDSGPSTSTQSSPAKKPRKQKVRTKILFEDDWSAQPSDRLDRIRYERFVKSITRSPRAEDEESEPESESSEMSPAEWGEMLGLITRGLEDEPIVLHCFETLEGLEDDTDGSLQSP*

..........................................................PGQSEPAEQSAFLETRGPMQAYTLILARTAYTAPFSFFX...........................VMGGEGLSRYNAKAIRSQLAFKWLX..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................

D1R54_gp2

MSGSSKASHARREQRTRSRSRSRSPPRCRRQNGGRCSASSRGDWRTNRSSSTASRRLKGSKTTPMEVFNRHKAETGINLSMCGFYWHSTRLARAGTDWIFNEGKPLFQSKCTNNLVSWDIVREMLFQFKKTMDQKYRNILYHGMRGADCDKCKYWDNVYLEHLANIETNDVVMQDISDEEMLSAAMEVDGTHE*

......................................................................................................................................................................................RPAIEVDRSHE*

D1R54_gp3

MAPTNRKPGGWVVPGFKYLGPFNPLNNGEPVNFVDAAAKAHDQAYQDIIDSGQNPYFSFNKADADFIETLSHDSSVGSWLGRSAFHLKKVLAPHLPQDGGEQPGPSGAKKPRLDPKQDRAQKRKLYFARSNKQAKQPRMSAGAEPTEDVAGSADPAAEGRAGGANGGGGGMGGGGGHGVGVSTGGWQAGTVFTDSAIITTGTRQWYAPIYNGHLYKLLKPDSGLHSNWTGISTPWGYFNFNEYDAHFSPQDWQRLLNEYKRWRPKSMHVKIYNLQIKQVVTLGADTLYNNDLTAGVHIFCDGSHQFPYSQHPWDTGVMPELPNKVWKLSQYAYFQALNDLIDTNAGSNADVGNIEKHIMKAAPFYILESASHQVLRTGEETSFTFEFDCGWVTNDRVYCPPQADFNPLVNTRRYFPTRQTGAGAANKFTYHRYNPYNKPSIWMPGPSLGYIGATQTSANPEKARGPVTVVYQPPYTTADGASANTEQNKDQQTLLPKLTEASMQNAGFDVAPVNNACNDLGYITMAYDSREESEQSTTITVKDVDADFARYGAVFVQDGTNKEIKADGTALTTQDRKNFSELRNVWMYPNQAWDATPISRDTPIWVKSPRTDRHTMFDTSDGTIPMAHPPGTIFVKVAKIPIPGDQDSYLNLYVTGQVTCQVIWEAERFQTKNWRPEVRTDVSAFSDPTLYTVNAAGVYNTPETFKEGMPTKRGINRVL*

IAATNRKPGGWVVPGFKYLGPFNPLSNGEPVNFVX................................................................................................................................................................................................WTGISTPWGYFNFNEYDAHFSPQDWQRLLNEYKRWRPKSMHVKIYNLQIKQVVTLGADTLY---XTAGVHIFCDGWDQLSYSEHPWDRGAMTELPYKVWKLX..................................FYILESASHQVLRTGEETSFTFEFDCGWVTNDRVYCPP--XFNPLVNTRRYFPTRQTGTGANNKXTYXRYNPYNKPSIWMPGPSPGYIGSTQTX......................................................HVNNACNDLGYITMAYDSREESEQSTTITVKDVDADFARYGAVFVX...................................................................................................................................................................

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	453	4706	18.9%	1746	87.8%	1012 (98.3%)	950 (92.2%)	0/18
Mutations:	525T>A, 552G>C, 677A>G, 3021T>A, 3022G>C, 3024T>G, 3030G>C, 3040G>C, 3044C>G, 3088A>G, 3114A>G, 3902_3911delAATAATGATT, 3912T>A, 3913G>A, 3945C>G, 3947C>G, 3955C>G, 3956C>T, 3965C>G, 3981C>G, 3982T>G, 3985T>G, 3987T>C, 3992C>A, 3997A>G, 4004A>T, 4189A>T, 4222T>C, 4228G>A, 4240A>G, 4241_4248delCAGGCAGA, 4273C>T, 4285C>T, 4297T>G, 4300A>G, 4301G>A, 4303G>T, 4306C>T, 4309C>A, 4310G>A, 4311C>A, 4312A>C, 4315C>T, 4321T>W, 4327C>Y, 4328C>K, 4330T>C, 4345T>C, 4354G>A, 4379T>C, 4380T>C, 4381G>A, 4384A>C, 4394G>A, 4395C>G, 4399T>A, 4402A>G, 4572C>A, 4585A>T, 4627G>A, 4630A>G, 4669G>A, 4675G>C, 4678T>C
CDS

D1R54_gp1	59	149	8.0%	397	95.0%	64 (100%)	60 (93.8%)	0/0/0/0	0
Protein mutations:	L83I (525T>A), A92P (552G>C)
Codon mutations:	TTA83ATA (525T>A), GCA92CCA (552G>C), AGA133AGG (677A>G)
D1R54_gp2	183	194	6.2%	44	61.1%	12 (100%)	7 (58.3%)	0/0/0/0	1
Protein mutations:	S183R (3021T>A), A184P (3022G>C 3024T>G), M186I (3030G>C), G190R (3040G>C), T191S (3044C>G)
Codon mutations:	AGT183AGA (3021T>A), GCT184CCG (3022G>C 3024T>G), ATG186ATC (3030G>C), GGC190CGC (3040G>C), ACC191AGC (3044C>G)
D1R54_gp3	1	557	38.2%	1604	76.9%	270 (98.2%)	247 (89.8%)	0/5/4/2	0
Protein mutations:	M1I (3040G>C), P3A (3044C>G), N26S (3114A>G), N289_D291del (3902_3911delAATAATGATT), S303W (3945C>G), H304D (3947C>G), F306L (3955C>G), P307S (3956C>T), Q310E (3965C>G), T315R (3981C>G 3982T>G), V317A (3987T>C), P319T (3992C>A), N323Y (4004A>T), Q402_A403del (4241_4248delCAGGCAGA), A422T (4301G>A 4303G>T), A425N (4310G>A 4311C>A 4312A>C), L448P (4379T>C 4380T>C 4381G>A), A453S (4394G>A 4395C>G), P512H (4572C>A)
Codon mutations:	ATG1ATC (3040G>C), CCC3GCC (3044C>G), AAA17AAG (3088A>G), AAT26AGT (3114A>G), AAT289_GAT291del (3902_3911delAATAATGATT), TTG292-AA (3902_3911delAATAATGATT 3912T>A 3913G>A), TCG303TGG (3945C>G), CAT304GAT (3947C>G), TTC306TTG (3955C>G), CCA307TCA (3956C>T), CAA310GAA (3965C>G), ACT315AGG (3981C>G 3982T>G), GGT316GGG (3985T>G), GTT317GCT (3987T>C), CCT319ACT (3992C>A), GAA320GAG (3997A>G), AAT323TAT (4004A>T), ACA384ACT (4189A>T), GAT395GAC (4222T>C), GTG397GTA (4228G>A), CCA401CCG (4240A>G), CAG402_GCA403del (4241_4248delCAGGCAGA), GAT404--T (4241_4248delCAGGCAGA), CGC412CGT (4273C>T), CCC416CCT (4285C>T), ACT420ACG (4297T>G), GGA421GGG (4300A>G), GCG422ACT (4301G>A 4303G>T), GGC423GGT (4306C>T), GCC424GCA (4309C>A), GCA425AAC (4310G>A 4311C>A 4312A>C), AAC426AAT (4315C>T), TTT428TTW (4321T>W), TAC430TAY (4327C>Y), CAT431KAC (4328C>K 4330T>C), TAT436TAC (4345T>C), CCG439CCA (4354G>A), TTG448CCA (4379T>C 4380T>C 4381G>A), GGA449GGC (4384A>C), GCC453AGC (4394G>A 4395C>G), ACT454ACA (4399T>A), CAA455CAG (4402A>G), CCT512CAT (4572C>A), GCA516GCT (4585A>T), AGG530AGA (4627G>A), GAA531GAG (4630A>G), GTG544GTA (4669G>A), GCG546GCC (4675G>C), GAT547GAC (4678T>C)
D1R54_gp4	90	419	41.2%	1360	75.3%	235 (97.9%)	216 (90.0%)	0/5/4/2	0
Protein mutations:	N151_D153del (3902_3911delAATAATGATT), S165W (3945C>G), H166D (3947C>G), F168L (3955C>G), P169S (3956C>T), Q172E (3965C>G), T177R (3981C>G 3982T>G), V179A (3987T>C), P181T (3992C>A), N185Y (4004A>T), Q264_A265del (4241_4248delCAGGCAGA), A284T (4301G>A 4303G>T), A287N (4310G>A 4311C>A 4312A>C), L310P (4379T>C 4380T>C 4381G>A), A315S (4394G>A 4395C>G), P374H (4572C>A)
Codon mutations:	AAT151_GAT153del (3902_3911delAATAATGATT), TTG154-AA (3902_3911delAATAATGATT 3912T>A 3913G>A), TCG165TGG (3945C>G), CAT166GAT (3947C>G), TTC168TTG (3955C>G), CCA169TCA (3956C>T), CAA172GAA (3965C>G), ACT177AGG (3981C>G 3982T>G), GGT178GGG (3985T>G), GTT179GCT (3987T>C), CCT181ACT (3992C>A), GAA182GAG (3997A>G), AAT185TAT (4004A>T), ACA246ACT (4189A>T), GAT257GAC (4222T>C), GTG259GTA (4228G>A), CCA263CCG (4240A>G), CAG264_GCA265del (4241_4248delCAGGCAGA), GAT266--T (4241_4248delCAGGCAGA), CGC274CGT (4273C>T), CCC278CCT (4285C>T), ACT282ACG (4297T>G), GGA283GGG (4300A>G), GCG284ACT (4301G>A 4303G>T), GGC285GGT (4306C>T), GCC286GCA (4309C>A), GCA287AAC (4310G>A 4311C>A 4312A>C), AAC288AAT (4315C>T), TTT290TTW (4321T>W), TAC292TAY (4327C>Y), CAT293KAC (4328C>K 4330T>C), TAT298TAC (4345T>C), CCG301CCA (4354G>A), TTG310CCA (4379T>C 4380T>C 4381G>A), GGA311GGC (4384A>C), GCC315AGC (4394G>A 4395C>G), ACT316ACA (4399T>A), CAA317CAG (4402A>G), CCT374CAT (4572C>A), GCA378GCT (4585A>T), AGG392AGA (4627G>A), GAA393GAG (4630A>G), GTG406GTA (4669G>A), GCG408GCC (4675G>C), GAT409GAC (4678T>C)
Proteins

NS1 (YP_009507354.1)	59	149	8.0%	397	95.0%	64 (100%)	60 (93.8%)	0/0/0/0	0
Protein mutations:	L83I (525T>A), A92P (552G>C)
Codon mutations:	TTA83ATA (525T>A), GCA92CCA (552G>C), AGA133AGG (677A>G)
NP (YP_009507355.1)	183	194	6.2%	44	61.1%	12 (100%)	7 (58.3%)	0/0/0/0	1
Protein mutations:	S183R (3021T>A), A184P (3022G>C 3024T>G), M186I (3030G>C), G190R (3040G>C), T191S (3044C>G)
Codon mutations:	AGT183AGA (3021T>A), GCT184CCG (3022G>C 3024T>G), ATG186ATC (3030G>C), GGC190CGC (3040G>C), ACC191AGC (3044C>G)
VP1 (YP_009507356.1)	1	557	38.2%	1604	76.9%	270 (98.2%)	247 (89.8%)	0/5/4/2	0
Protein mutations:	M1I (3040G>C), P3A (3044C>G), N26S (3114A>G), N289_D291del (3902_3911delAATAATGATT), S303W (3945C>G), H304D (3947C>G), F306L (3955C>G), P307S (3956C>T), Q310E (3965C>G), T315R (3981C>G 3982T>G), V317A (3987T>C), P319T (3992C>A), N323Y (4004A>T), Q402_A403del (4241_4248delCAGGCAGA), A422T (4301G>A 4303G>T), A425N (4310G>A 4311C>A 4312A>C), L448P (4379T>C 4380T>C 4381G>A), A453S (4394G>A 4395C>G), P512H (4572C>A)
Codon mutations:	ATG1ATC (3040G>C), CCC3GCC (3044C>G), AAA17AAG (3088A>G), AAT26AGT (3114A>G), AAT289_GAT291del (3902_3911delAATAATGATT), TTG292-AA (3902_3911delAATAATGATT 3912T>A 3913G>A), TCG303TGG (3945C>G), CAT304GAT (3947C>G), TTC306TTG (3955C>G), CCA307TCA (3956C>T), CAA310GAA (3965C>G), ACT315AGG (3981C>G 3982T>G), GGT316GGG (3985T>G), GTT317GCT (3987T>C), CCT319ACT (3992C>A), GAA320GAG (3997A>G), AAT323TAT (4004A>T), ACA384ACT (4189A>T), GAT395GAC (4222T>C), GTG397GTA (4228G>A), CCA401CCG (4240A>G), CAG402_GCA403del (4241_4248delCAGGCAGA), GAT404--T (4241_4248delCAGGCAGA), CGC412CGT (4273C>T), CCC416CCT (4285C>T), ACT420ACG (4297T>G), GGA421GGG (4300A>G), GCG422ACT (4301G>A 4303G>T), GGC423GGT (4306C>T), GCC424GCA (4309C>A), GCA425AAC (4310G>A 4311C>A 4312A>C), AAC426AAT (4315C>T), TTT428TTW (4321T>W), TAC430TAY (4327C>Y), CAT431KAC (4328C>K 4330T>C), TAT436TAC (4345T>C), CCG439CCA (4354G>A), TTG448CCA (4379T>C 4380T>C 4381G>A), GGA449GGC (4384A>C), GCC453AGC (4394G>A 4395C>G), ACT454ACA (4399T>A), CAA455CAG (4402A>G), CCT512CAT (4572C>A), GCA516GCT (4585A>T), AGG530AGA (4627G>A), GAA531GAG (4630A>G), GTG544GTA (4669G>A), GCG546GCC (4675G>C), GAT547GAC (4678T>C)
VP2 (YP_009507357.1)	90	419	41.2%	1360	75.3%	235 (97.9%)	216 (90.0%)	0/5/4/2	0
Protein mutations:	N151_D153del (3902_3911delAATAATGATT), S165W (3945C>G), H166D (3947C>G), F168L (3955C>G), P169S (3956C>T), Q172E (3965C>G), T177R (3981C>G 3982T>G), V179A (3987T>C), P181T (3992C>A), N185Y (4004A>T), Q264_A265del (4241_4248delCAGGCAGA), A284T (4301G>A 4303G>T), A287N (4310G>A 4311C>A 4312A>C), L310P (4379T>C 4380T>C 4381G>A), A315S (4394G>A 4395C>G), P374H (4572C>A)
Codon mutations:	AAT151_GAT153del (3902_3911delAATAATGATT), TTG154-AA (3902_3911delAATAATGATT 3912T>A 3913G>A), TCG165TGG (3945C>G), CAT166GAT (3947C>G), TTC168TTG (3955C>G), CCA169TCA (3956C>T), CAA172GAA (3965C>G), ACT177AGG (3981C>G 3982T>G), GGT178GGG (3985T>G), GTT179GCT (3987T>C), CCT181ACT (3992C>A), GAA182GAG (3997A>G), AAT185TAT (4004A>T), ACA246ACT (4189A>T), GAT257GAC (4222T>C), GTG259GTA (4228G>A), CCA263CCG (4240A>G), CAG264_GCA265del (4241_4248delCAGGCAGA), GAT266--T (4241_4248delCAGGCAGA), CGC274CGT (4273C>T), CCC278CCT (4285C>T), ACT282ACG (4297T>G), GGA283GGG (4300A>G), GCG284ACT (4301G>A 4303G>T), GGC285GGT (4306C>T), GCC286GCA (4309C>A), GCA287AAC (4310G>A 4311C>A 4312A>C), AAC288AAT (4315C>T), TTT290TTW (4321T>W), TAC292TAY (4327C>Y), CAT293KAC (4328C>K 4330T>C), TAT298TAC (4345T>C), CCG301CCA (4354G>A), TTG310CCA (4379T>C 4380T>C 4381G>A), GGA311GGC (4384A>C), GCC315AGC (4394G>A 4395C>G), ACT316ACA (4399T>A), CAA317CAG (4402A>G), CCT374CAT (4572C>A), GCA378GCT (4585A>T), AGG392AGA (4627G>A), GAA393GAG (4630A>G), GTG406GTA (4669G>A), GCG408GCC (4675G>C), GAT409GAC (4678T>C)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43