Genome Detective

NGS Details (SRR3458562_Metagenome_example): Bat rotavirus (segment 7)

Assembly

Coverage Length

275 (1 contig(s))

Depth Of Coverage

1027.4

Number Of Reads

3526

Reads Per Million

227.51 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

Bat rotavirus (Taxonomy ID: 1340801)

Reference Genome

NC_040405.1

NT Identity (%)

82.7839

AA Identity (%)

84.7826

Number Of Stop Codons

Number Of CDS

Alignment

Segment

segment 7

Alignment Score

347.0 (NT) + 401.0 (AA) = 748.0

Concordance (%)

75.7782

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 267 and ends at position 541 relative to NC_040405.1 reference sequence.

NC_040405.1

SRR3458562_Metagenome_example-NC_040405.1-97-0

NC_040405.1

SRR3458562_Metagenome_example-NC_040405.1-97-0

ATGCTCAAGATGGAGTCTACGCAACAGATGGCCGTCTCAATTATTAACTCTTCTTTTGAAGCTGCAGTTGTAGCTGCAACCTCAGCTCTTGAGAATATGGGTATACAATATGATCATAATGAGGTGTATACTAGAGTAAAAAGCAAGTTTGATTTTATCATGGATGATTCAGGAGTCAAAAACAATCTGATCGGCAAAGCGGTTACTATTGACCAAGCTTTAAATGGGAAATTTGCTTCAGCTATCAGAAATAGAAACTGGATGAATGATTCTCATACAGTAGCCAGGTTGGATGAGGATGTGAACAAATTGAGAATGATGTTATCATCAAAAGGAATAGATCAAAAAATTAGAGTTCTAAATGCATGTTTTAGTGTCAAAAGGGTGCCTGGAAAGTCGTCATCAATAATAAAGTGTAGTAGGTTAATGAAAGAAAAAATTGAACGTGGCGAAATTGAAGTTGATGATTCTTTTGTTGAAGAAAAAATGGAGATCGACACAATCGATTGGAAAACTAGGTATGAGCAATTGGAAAAGAGATTTGAATCATTAAAATGTAGAGTGAACGAAAAATACAATAGTTGGGTTGTTAAAGCTCGGAAAGTAAATGAGACTGTGCATTCACTGCAGAGTGTGATATCCAGGCAACAGGCTCATATTAGCGATTTGCAATCATATAATGACAAATTGGAACGTGATTTGCAATCCAAAGTCGAATCTGTGGTTTCATCAATTGAGTGGTATTTACGATCTATGGAGTTACCAGAGGATGTTAAAACGGACATAGAACAGCAGCTTAATTCTGTAGATCGAATGAATGTGTTGAGCGCATTTGACGATTTTGAACTGATTATTCGGAATCTAATTTCTGACTATGATAAAGTGTTTTTAATGTTCAAGGGACTATTACAGCGGTGTAATTATAGTTATACATATGAGTAA

..........................................................................................................................................................................................................................................................................TGATTCTCAAACTACAGATAGACTAGATGAAGATGTGAACAAACTTAGAATGATGTTATCATCTAAAGGAATTGATCAAAAAATGAGAGTACTTAATGCATGT--TAGTGTGAAGAGAGCTCCAGGTAAATCATCATCAATAATTAAATGTACTAGACTAATGAGAGATAAGATTGAACGTGGTGAAGTCGAAGTGGATGATTCGTTTGTTGAAGAAAAAATGGAAGTTGACACAATTGATTGGAAATCTAGGTATGAACAATTGTGAAAGAGAT.................................................................................................................................................................................................................................................................................................................................................................................................................

100

200

300

400

500

600

700

800

900

NSP3

MLKMESTQQMAVSIINSSFEAAVVAATSALENMGIQYDHNEVYTRVKSKFDFIMDDSGVKNNLIGKAVTIDQALNGKFASAIRNRNWMNDSHTVARLDEDVNKLRMMLSSKGIDQKIRVLNACFSVKRVPGKSSSIIKCSRLMKEKIERGEIEVDDSFVEEKMEIDTIDWKTRYEQLEKRFESLKCRVNEKYNSWVVKARKVNETVHSLQSVISRQQAHISDLQSYNDKLERDLQSKVESVVSSIEWYLRSMELPEDVKTDIEQQLNSVDRMNVLSAFDDFELIIRNLISDYDKVFLMFKGLLQRCNYSYTYE*

........................................................................................XDSQTTDRLDEDVNKLRMMLSSKGIDQKMRVLNACXSVKRAPGKSSSIIKCTRLMRDKIERGEVEVDDSFVEEKMEVDTIDWKSRYEQL*KRX.....................................................................................................................................

Alignment Detailed Statistics


	Begin	End	Coverage	Score	Concordance	Matches	Identities	I/D/M/F^*	Stop Codons
NT	267	541	29.2%	347	64.9%	273 (99.3%)	226 (82.2%)	0/2
Mutations:	276T>A 279A>T 280G>A 281T>C 284C>A 285C>T 288G>A 289T>C 291G>A 297G>A 310T>C 312G>T 330A>T 339A>T 351T>G 357T>A 360A>T 370_371delTT 378C>G 381A>G 384G>A 386T>C 387G>T 390T>A 393A>T 396G>A 399G>A 411A>T 414G>A 419G>C 423G>A 424T>C 431A>G 435A>T 438A>G 450C>T 454A>G 456T>C 462T>G 471T>G 492G>A 493A>G 495C>T 504C>T 514A>T 525G>A 532G>T 533A>G
CDS

NSP3	90	181	29.3%	401	65.5%	92 (100%)	78 (84.8%)	0/0/1/1	1
Protein mutations:	H92Q (276T>A) V94T (280G>A 281T>C) A95D (284C>A 285C>T) I117M (351T>G) V129A (386T>C 387G>T) S140T (419G>C) K144R (431A>G) E145D (435A>T) I152V (454A>G 456T>C) I165V (493A>G 495C>T) T172S (514A>T) E178* (532G>T 533A>G)
Codon mutations:	CAT92CAA (276T>A) ACA93ACT (279A>T) GTA94ACA (280G>A 281T>C) GCC95GAT (284C>A 285C>T) AGG96AGA (288G>A) TTG97CTA (289T>C 291G>A) GAG99GAA (297G>A) TTG104CTT (310T>C 312G>T) TCA110TCT (330A>T) ATA113ATT (339A>T) ATT117ATG (351T>G) GTT119GTA (357T>A) CTA120CTT (360A>T) TTT124--T (370_371delTT) GTC126GTG (378C>G) AAA127AAG (381A>G) AGG128AGA (384G>A) GTG129GCT (386T>C 387G>T) CCT130CCA (390T>A) GGA131GGT (393A>T) AAG132AAA (396G>A) TCG133TCA (399G>A) ATA137ATT (411A>T) AAG138AAA (414G>A) AGT140ACT (419G>C) AGG141AGA (423G>A) TTA142CTA (424T>C) AAA144AGA (431A>G) GAA145GAT (435A>T) AAA146AAG (438A>G) GGC150GGT (450C>T) ATT152GTC (454A>G 456T>C) GTT154GTG (462T>G) TCT157TCG (471T>G) GAG164GAA (492G>A) ATC165GTT (493A>G 495C>T) ATC168ATT (504C>T) ACT172TCT (514A>T) GAG175GAA (525G>A) GAA178TGA (532G>T 533A>G)
Proteins

NSP3 (YP_009551531.1)	90	181	29.3%	401	65.5%	92 (100%)	78 (84.8%)	0/0/1/1	1
Protein mutations:	H92Q (276T>A) V94T (280G>A 281T>C) A95D (284C>A 285C>T) I117M (351T>G) V129A (386T>C 387G>T) S140T (419G>C) K144R (431A>G) E145D (435A>T) I152V (454A>G 456T>C) I165V (493A>G 495C>T) T172S (514A>T) E178* (532G>T 533A>G)
Codon mutations:	CAT92CAA (276T>A) ACA93ACT (279A>T) GTA94ACA (280G>A 281T>C) GCC95GAT (284C>A 285C>T) AGG96AGA (288G>A) TTG97CTA (289T>C 291G>A) GAG99GAA (297G>A) TTG104CTT (310T>C 312G>T) TCA110TCT (330A>T) ATA113ATT (339A>T) ATT117ATG (351T>G) GTT119GTA (357T>A) CTA120CTT (360A>T) TTT124--T (370_371delTT) GTC126GTG (378C>G) AAA127AAG (381A>G) AGG128AGA (384G>A) GTG129GCT (386T>C 387G>T) CCT130CCA (390T>A) GGA131GGT (393A>T) AAG132AAA (396G>A) TCG133TCA (399G>A) ATA137ATT (411A>T) AAG138AAA (414G>A) AGT140ACT (419G>C) AGG141AGA (423G>A) TTA142CTA (424T>C) AAA144AGA (431A>G) GAA145GAT (435A>T) AAA146AAG (438A>G) GGC150GGT (450C>T) ATT152GTC (454A>G 456T>C) GTT154GTG (462T>G) TCT157TCG (471T>G) GAG164GAA (492G>A) ATC165GTT (493A>G 495C>T) ATC168ATT (504C>T) ACT172TCT (514A>T) GAG175GAA (525G>A) GAA178TGA (532G>T 533A>G)

^*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43