Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Lederbergvirus Sf6

Assembly

3739 (8 contig(s))
24.9
905
58.39 rpm (after QC)
0
de novo + reference guided assembly
Bcf Tools

Coverage Map

Variant Tables

Assignment

Lederbergvirus Sf6 (Taxonomy ID: 10761)
94.8559
95.5537
6
66

Alignment

6600.0 (NT) + 7528.0 (AA) = 14128.0
92.9996
Local, heuristic, nucleotide (BLASTN)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT1442360169.6%660089.6%3713 (99.3%)3522 (94.2%)0/26
Mutations:1487G>A, 1505A>G, 1559T>C, 1580A>C, 1595T>C, 1634G>A, 1676C>T, 1685G>A, 1694A>T, 7015T>C, 7041A>G, 7063T>C, 7081C>A, 7090G>A, 7099T>C, 7102T>C, 7136A>C, 7138G>A, 7150A>T, 7183C>T, 7228C>T, 7252C>T, 7258C>T, 7306C>A, 7348T>C, 7357T>A, 7363C>T, 7375T>C, 7378C>A, 7381G>A, 7384T>G, 7485C>T, 7543G>A, 7546T>C, 7549C>T, 7561G>A, 7564T>C, 7573G>C, 7600G>A, 7615G>A, 7618T>C, 7627C>T, 7633T>G, 7672C>T, 7675C>T, 7714G>T, 7717A>G, 7718T>G, 7720T>C, 7721C>G, 7726G>A, 7735T>G, 7742T>C, 7756C>T, 7762T>G, 7771T>C, 7777G>A, 7803G>C, 9341C>A, 9371T>C, 9398G>A, 9401C>T, 9422T>C, 9425T>G, 9598T>C, 9612G>A, 13778T>G, 13855A>G, 13877T>C, 13886A>C, 13895C>T, 13904T>G, 13907G>A, 13913T>C, 13914G>A, 13916T>C, 13919C>T, 13922T>C, 13928C>T, 13931A>T, 13934T>C, 13940G>A, 13943C>T, 13949G>A, 13951A>G, 13961A>G, 13964T>C, 13972A>T, 13985A>T, 13994A>G, 13997T>C, 14009T>C, 14010T>G, 14011C>T, 14012G>A, 14027T>C, 14045C>T, 14048C>T, 18278A>T, 18308A>G, 18371C>T, 18488G>A, 32881A>T, 32882A>T, 32892A>T, 32903A>T, 32907A>C, 32929A>G, 32935C>T, 32947G>T, 32959G>A, 32983A>G, 33013G>T, 33025C>A, 33040G>A, 33043A>G, 33047A>G, 33048C>T, 33050A>G, 33052C>T, 33057T>C, 33088T>C, 33118G>A, 33124G>A, 33136T>C, 33143T>C, 33156A>G, 33193C>T, 33201T>C, 33202delG, 33218C>A, 33253C>T, 33265G>A, 33359G>A, 33400C>T, 33403G>C, 33406C>T, 33418C>T, 33420T>G, 33421T>C, 33427G>A, 33429A>G, 33430G>A, 33433A>C, 33445A>G, 33448T>C, 33457A>G, 33463T>C, 33487A>G, 33490G>A, 33548C>T, 33562C>A, 33575C>T, 33577T>C, 33586_33603delGGCCGAACCGTGGCTGAT, 33609G>T, 33610T>A, 33618G>T, 33628G>A, 33646G>A, 33652delT, 33653G>T, 33654G>T, 33676G>A, 33678A>C, 33691G>T, 33699C>T, 33702C>T, 33704A>C, 33715G>A, 33720T>C, 33723C>T, 33727A>C, 33728G>A, 33745T>C, 33749C>T, 33768C>T, 33792G>A, 33846G>C, 33851C>T, 33855G>T, 33861A>G, 33870C>T, 33873G>T, 33876A>T, 33879G>C, 33882G>A, 33991T>G, 34117G>A, 34118T>A, 34119G>A, 34126_34131delCAAACC, 34132A>C, 35977G>A, 35994G>T
CDS
34243720.4%62198.4%96 (100%)95 (99.0%)0/0/0/00
5733158.1%187198.2%275 (100%)268 (97.5%)0/0/0/00
Protein mutations:N69S (7041A>G), A217V (7485C>T), M293I (7714G>T), S295A (7718T>G 7720T>C), L296V (7721C>G), G323A (7803G>C)
Codon mutations:CGT60CGC (7015T>C), AAT69AGT (7041A>G), GGT76GGC (7063T>C), GGC82GGA (7081C>A), GAG85GAA (7090G>A), GAT88GAC (7099T>C), GTT89GTC (7102T>C), AGG101CGA (7136A>C 7138G>A), GCA105GCT (7150A>T), CGC116CGT (7183C>T), AGC131AGT (7228C>T), GGC139GGT (7252C>T), GTC141GTT (7258C>T), GGC157GGA (7306C>A), CAT171CAC (7348T>C), CGT174CGA (7357T>A), AGC176AGT (7363C>T), CGT180CGC (7375T>C), GCC181GCA (7378C>A), GAG182GAA (7381G>A), TCT183TCG (7384T>G), GCT217GTT (7485C>T), GGG236GGA (7543G>A), ACT237ACC (7546T>C), TAC238TAT (7549C>T), CCG242CCA (7561G>A), TTT243TTC (7564T>C), TCG246TCC (7573G>C), ACG255ACA (7600G>A), GTG260GTA (7615G>A), TAT261TAC (7618T>C), GGC264GGT (7627C>T), GGT266GGG (7633T>G), ATC279ATT (7672C>T), CTC280CTT (7675C>T), ATG293ATT (7714G>T), GAA294GAG (7717A>G), TCT295GCC (7718T>G 7720T>C), CTG296GTG (7721C>G), CGG297CGA (7726G>A), GCT300GCG (7735T>G), TTG303CTG (7742T>C), CAC307CAT (7756C>T), CCT309CCG (7762T>G), GTT312GTC (7771T>C), GTG314GTA (7777G>A), GGT323GCT (7803G>C)
7315252.6%56298.9%80 (100%)80 (100%)0/0/0/01
14417.3%21780.7%40 (100%)37 (92.5%)0/0/0/00
Protein mutations:C18Y (9612G>A)
Codon mutations:GGT13GGC (9598T>C), TGC18TAC (9612G>A)
1211516.7%71296.6%104 (100%)99 (95.2%)0/0/0/00
Protein mutations:Q46R (13855A>G), V66I (13914G>A 13916T>C), Q78R (13951A>G), E85V (13972A>T), S98V (14010T>G 14011C>T 14012G>A)
Codon mutations:GCT20GCG (13778T>G), CAG46CGG (13855A>G), AAT53AAC (13877T>C), GGA56GGC (13886A>C), GTC59GTT (13895C>T), TCT62TCG (13904T>G), CAG63CAA (13907G>A), ATT65ATC (13913T>C), GTT66ATC (13914G>A 13916T>C), ATC67ATT (13919C>T), AAT68AAC (13922T>C), GCC70GCT (13928C>T), GGA71GGT (13931A>T), TAT72TAC (13934T>C), GTG74GTA (13940G>A), TAC75TAT (13943C>T), GGG77GGA (13949G>A), CAG78CGG (13951A>G), AAA81AAG (13961A>G), TTT82TTC (13964T>C), GAG85GTG (13972A>T), TCA89TCT (13985A>T), GTA92GTG (13994A>G), TAT93TAC (13997T>C), GGT97GGC (14009T>C), TCG98GTA (14010T>G 14011C>T 14012G>A), TTT103TTC (14027T>C), TAC109TAT (14045C>T), GAC110GAT (14048C>T)
12144.7%12891.4%21 (100%)20 (95.2%)0/0/0/00
167100%478100%67 (100%)67 (100%)0/0/0/01
1041041.0%114.3%1 (100%)1 (100%)0/0/0/01
33382.9%-102-212.5%6 (100%)3 (50.0%)0/0/1/10
Protein mutations:K35Q (34132A>C)
Codon mutations:ACC34AC- (34126_34131delCAAACC), AAG35CAG (34132A>C)
1307100%178279.4%301 (98.0%)272 (88.6%)0/6/2/21
Protein mutations:R6C (33792G>A), E14K (33768C>T), G20E (33749C>T), P27L (33727A>C 33728G>A), V29I (33723C>T), T30A (33720T>C), F35C (33704A>C), G36R (33702C>T), V37I (33699C>T), Y44D (33676G>A 33678A>C), L64I (33618G>T), H67N (33609G>T), I69_A74del (33586_33603delGGCCGAACCGTGGCTGAT), S78N (33575C>T), M82I (33562C>A), G87D (33548C>T), Y127H (33427G>A 33429A>G), T150M (33359G>A), G197V (33218C>A), S203G (33201T>C), Q222R (33143T>C), M251V (33057T>C), V253A (33050A>G), V254T (33047A>G 33048C>T), E261D (33025C>A), S301A (32907A>C), V302E (32903A>T), C306S (32892A>T)
Codon mutations:CGC6TGC (33792G>A), GAA14AAA (33768C>T), GGG20GAG (33749C>T), AAA21AAG (33745T>C), CCT27CTG (33727A>C 33728G>A), GTC29ATC (33723C>T), ACA30GCA (33720T>C), CTC31CTT (33715G>A), TTC35TGC (33704A>C), GGG36AGG (33702C>T), GTT37ATT (33699C>T), CGC39CGA (33691G>T), TAC44GAT (33676G>A 33678A>C), CCA52AA- (33652delT 33653G>T 33654G>T), GGC54GGT (33646G>A), CGC60CGT (33628G>A), CTT64ATT (33618G>T), CTA66CTT (33610T>A), CAT67AAT (33609G>T), ATC69_GCC74del (33586_33603delGGCCGAACCGTGGCTGAT), AGA77AGG (33577T>C), AGC78AAC (33575C>T), ATG82ATT (33562C>A), GGC87GAC (33548C>T), AGC106AGT (33490G>A), TGT107TGC (33487A>G), AAA115AAG (33463T>C), GGT117GGC (33457A>G), GAA120GAG (33448T>C), CAT121CAC (33445A>G), CCT125CCG (33433A>C), AAC126AAT (33430G>A), TAC127CAT (33427G>A 33429A>G), GAA129GAG (33421T>C), AGG130CGA (33418C>T 33420T>G), GTG134GTA (33406C>T), ACC135ACG (33403G>C), GAG136GAA (33400C>T), ACG150ATG (33359G>A), CTC181CTT (33265G>A), GCG185GCA (33253C>T), GGC197GTC (33218C>A), CAC202CA- (33202delG), AGC203GGC (33201T>C), CAG205CAA (33193C>T), TTG218CTG (33156A>G), CAG222CGG (33143T>C), AGA224AGG (33136T>C), AGC228AGT (33124G>A), CGC230CGT (33118G>A), GAA240GAG (33088T>C), ATG251GTG (33057T>C), CCG252CCA (33052C>T), GTG253GCG (33050A>G), GTG254ACG (33047A>G 33048C>T), GGT255GGC (33043A>G), TAC256TAT (33040G>A), GAG261GAT (33025C>A), GCC265GCA (33013G>T), AGT275AGC (32983A>G), AAC283AAT (32959G>A), CCC287CCA (32947G>T), TCG291TCA (32935C>T), AAT293AAC (32929A>G), TCG301GCG (32907A>C), GTG302GAG (32903A>T), TGT306AGT (32892A>T)
1101100%60098.5%101 (100%)99 (98.0%)0/0/0/01
Protein mutations:K22T (33991T>G), E69K (33851C>T)
Codon mutations:AAA22ACA (33991T>G), TCC58TCT (33882G>A), CCC59CCG (33879G>C), ATT60ATA (33876A>T), ACC61ACA (33873G>T), CCG62CCA (33870C>T), ATT65ATC (33861A>G), ATC67ATA (33855G>T), GAG69AAG (33851C>T), CTC70CTG (33846G>C), ACC88ACT (33792G>A), CTG96CTA (33768C>T)
7417357.8%65898.2%100 (100%)98 (98.0%)0/0/0/01
Protein mutations:S165N (35977G>A), A171S (35994G>T)
Codon mutations:AGC165AAC (35977G>A), GCC171TCC (35994G>T)
Proteins
34243720.4%62198.4%96 (100%)95 (99.0%)0/0/0/00
Protein mutations:none
Codon mutations:GTG356GTA (1487G>A), GCA362GCG (1505A>G), GTT380GTC (1559T>C), CCA387CCC (1580A>C), AGT392AGC (1595T>C), AAG405AAA (1634G>A), AAC419AAT (1676C>T), AAG422AAA (1685G>A), CTA425CTT (1694A>T)
5733158.1%187198.2%275 (100%)268 (97.5%)0/0/0/00
Protein mutations:N69S (7041A>G), A217V (7485C>T), M293I (7714G>T), S295A (7718T>G 7720T>C), L296V (7721C>G), G323A (7803G>C)
Codon mutations:CGT60CGC (7015T>C), AAT69AGT (7041A>G), GGT76GGC (7063T>C), GGC82GGA (7081C>A), GAG85GAA (7090G>A), GAT88GAC (7099T>C), GTT89GTC (7102T>C), AGG101CGA (7136A>C 7138G>A), GCA105GCT (7150A>T), CGC116CGT (7183C>T), AGC131AGT (7228C>T), GGC139GGT (7252C>T), GTC141GTT (7258C>T), GGC157GGA (7306C>A), CAT171CAC (7348T>C), CGT174CGA (7357T>A), AGC176AGT (7363C>T), CGT180CGC (7375T>C), GCC181GCA (7378C>A), GAG182GAA (7381G>A), TCT183TCG (7384T>G), GCT217GTT (7485C>T), GGG236GGA (7543G>A), ACT237ACC (7546T>C), TAC238TAT (7549C>T), CCG242CCA (7561G>A), TTT243TTC (7564T>C), TCG246TCC (7573G>C), ACG255ACA (7600G>A), GTG260GTA (7615G>A), TAT261TAC (7618T>C), GGC264GGT (7627C>T), GGT266GGG (7633T>G), ATC279ATT (7672C>T), CTC280CTT (7675C>T), ATG293ATT (7714G>T), GAA294GAG (7717A>G), TCT295GCC (7718T>G 7720T>C), CTG296GTG (7721C>G), CGG297CGA (7726G>A), GCT300GCG (7735T>G), TTG303CTG (7742T>C), CAC307CAT (7756C>T), CCT309CCG (7762T>G), GTT312GTC (7771T>C), GTG314GTA (7777G>A), GGT323GCT (7803G>C)
7315252.6%56298.9%80 (100%)80 (100%)0/0/0/01
Protein mutations:none
Codon mutations:ATC80ATA (9341C>A), ACT90ACC (9371T>C), TCG99TCA (9398G>A), TTC100TTT (9401C>T), CAT107CAC (9422T>C), GGT108GGG (9425T>G)
14417.3%21780.7%40 (100%)37 (92.5%)0/0/0/00
Protein mutations:C18Y (9612G>A)
Codon mutations:GGT13GGC (9598T>C), TGC18TAC (9612G>A)
1211516.7%71296.6%104 (100%)99 (95.2%)0/0/0/00
Protein mutations:Q46R (13855A>G), V66I (13914G>A 13916T>C), Q78R (13951A>G), E85V (13972A>T), S98V (14010T>G 14011C>T 14012G>A)
Codon mutations:GCT20GCG (13778T>G), CAG46CGG (13855A>G), AAT53AAC (13877T>C), GGA56GGC (13886A>C), GTC59GTT (13895C>T), TCT62TCG (13904T>G), CAG63CAA (13907G>A), ATT65ATC (13913T>C), GTT66ATC (13914G>A 13916T>C), ATC67ATT (13919C>T), AAT68AAC (13922T>C), GCC70GCT (13928C>T), GGA71GGT (13931A>T), TAT72TAC (13934T>C), GTG74GTA (13940G>A), TAC75TAT (13943C>T), GGG77GGA (13949G>A), CAG78CGG (13951A>G), AAA81AAG (13961A>G), TTT82TTC (13964T>C), GAG85GTG (13972A>T), TCA89TCT (13985A>T), GTA92GTG (13994A>G), TAT93TAC (13997T>C), GGT97GGC (14009T>C), TCG98GTA (14010T>G 14011C>T 14012G>A), TTT103TTC (14027T>C), TAC109TAT (14045C>T), GAC110GAT (14048C>T)
12144.7%12891.4%21 (100%)20 (95.2%)0/0/0/00
Protein mutations:none
Codon mutations:none
167100%478100%67 (100%)67 (100%)0/0/0/01
Protein mutations:none
Codon mutations:CAG6CAA (18371C>T), ATT27ATC (18308A>G), CCT37CCA (18278A>T)
1041041.0%114.3%1 (100%)1 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
33382.9%-102-212.5%6 (100%)3 (50.0%)0/0/1/10
Protein mutations:K35Q (34132A>C)
Codon mutations:ACC34AC- (34126_34131delCAAACC), AAG35CAG (34132A>C)
1307100%178279.4%301 (98.0%)272 (88.6%)0/6/2/21
Protein mutations:R6C (33792G>A), E14K (33768C>T), G20E (33749C>T), P27L (33727A>C 33728G>A), V29I (33723C>T), T30A (33720T>C), F35C (33704A>C), G36R (33702C>T), V37I (33699C>T), Y44D (33676G>A 33678A>C), L64I (33618G>T), H67N (33609G>T), I69_A74del (33586_33603delGGCCGAACCGTGGCTGAT), S78N (33575C>T), M82I (33562C>A), G87D (33548C>T), Y127H (33427G>A 33429A>G), T150M (33359G>A), G197V (33218C>A), S203G (33201T>C), Q222R (33143T>C), M251V (33057T>C), V253A (33050A>G), V254T (33047A>G 33048C>T), E261D (33025C>A), S301A (32907A>C), V302E (32903A>T), C306S (32892A>T)
Codon mutations:CGC6TGC (33792G>A), GAA14AAA (33768C>T), GGG20GAG (33749C>T), AAA21AAG (33745T>C), CCT27CTG (33727A>C 33728G>A), GTC29ATC (33723C>T), ACA30GCA (33720T>C), CTC31CTT (33715G>A), TTC35TGC (33704A>C), GGG36AGG (33702C>T), GTT37ATT (33699C>T), CGC39CGA (33691G>T), TAC44GAT (33676G>A 33678A>C), CCA52AA- (33652delT 33653G>T 33654G>T), GGC54GGT (33646G>A), CGC60CGT (33628G>A), CTT64ATT (33618G>T), CTA66CTT (33610T>A), CAT67AAT (33609G>T), ATC69_GCC74del (33586_33603delGGCCGAACCGTGGCTGAT), AGA77AGG (33577T>C), AGC78AAC (33575C>T), ATG82ATT (33562C>A), GGC87GAC (33548C>T), AGC106AGT (33490G>A), TGT107TGC (33487A>G), AAA115AAG (33463T>C), GGT117GGC (33457A>G), GAA120GAG (33448T>C), CAT121CAC (33445A>G), CCT125CCG (33433A>C), AAC126AAT (33430G>A), TAC127CAT (33427G>A 33429A>G), GAA129GAG (33421T>C), AGG130CGA (33418C>T 33420T>G), GTG134GTA (33406C>T), ACC135ACG (33403G>C), GAG136GAA (33400C>T), ACG150ATG (33359G>A), CTC181CTT (33265G>A), GCG185GCA (33253C>T), GGC197GTC (33218C>A), CAC202CA- (33202delG), AGC203GGC (33201T>C), CAG205CAA (33193C>T), TTG218CTG (33156A>G), CAG222CGG (33143T>C), AGA224AGG (33136T>C), AGC228AGT (33124G>A), CGC230CGT (33118G>A), GAA240GAG (33088T>C), ATG251GTG (33057T>C), CCG252CCA (33052C>T), GTG253GCG (33050A>G), GTG254ACG (33047A>G 33048C>T), GGT255GGC (33043A>G), TAC256TAT (33040G>A), GAG261GAT (33025C>A), GCC265GCA (33013G>T), AGT275AGC (32983A>G), AAC283AAT (32959G>A), CCC287CCA (32947G>T), TCG291TCA (32935C>T), AAT293AAC (32929A>G), TCG301GCG (32907A>C), GTG302GAG (32903A>T), TGT306AGT (32892A>T)
1101100%60098.5%101 (100%)99 (98.0%)0/0/0/01
Protein mutations:K22T (33991T>G), E69K (33851C>T)
Codon mutations:AAA22ACA (33991T>G), TCC58TCT (33882G>A), CCC59CCG (33879G>C), ATT60ATA (33876A>T), ACC61ACA (33873G>T), CCG62CCA (33870C>T), ATT65ATC (33861A>G), ATC67ATA (33855G>T), GAG69AAG (33851C>T), CTC70CTG (33846G>C), ACC88ACT (33792G>A), CTG96CTA (33768C>T)
7417357.8%65898.2%100 (100%)98 (98.0%)0/0/0/01
Protein mutations:S165N (35977G>A), A171S (35994G>T)
Codon mutations:AGC165AAC (35977G>A), GCC171TCC (35994G>T)
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43