Version 2.16.3
Genome Detective Platform

NGS Details (SRR3458562_Metagenome_example): Shigella phage SfIV

Assembly

18365 (50 contig(s))
8.6
1453
93.75 rpm (after QC)
0
read mapping against reference + variant calling
Bcf Tools

Coverage Map

Variant Tables

Assignment

Shigella phage SfIV (Taxonomy ID: 1407493)
99.3956
98.8707
22
54

Alignment

36286.0 (NT) + 39444.0 (AA) = 75730.0
99.1451
Local, heuristic, nucleotide (BLASTN)

Alignment Detailed Statistics

BeginEndCoverageScoreConcordanceMatchesIdentitiesI/D/M/F*Stop Codons
NT2083945946.2%3628698.8%18365 (100%)18254 (99.4%)0/0
Mutations:2157G>A, 2230C>T, 2274T>C, 2939C>T, 2944T>C, 3007A>T, 3058G>A, 3061A>T, 3100C>T, 3199C>T, 3559C>T, 3613G>C, 3625T>G, 4377T>G, 4486G>A, 4690A>G, 5104G>T, 5227A>T, 5786A>G, 5885T>C, 6018T>A, 6229A>T, 6277C>T, 6279G>A, 7346T>C, 7460C>A, 7563C>T, 8374C>T, 8417G>T, 8569T>C, 8666T>C, 8708T>C, 8799C>A, 13343C>T, 13346T>C, 13949A>G, 13982C>T, 14017C>G, 14135G>A, 14234T>C, 14273T>C, 14333G>A, 14419G>T, 14546A>G, 14623C>T, 15536A>G, 15752A>G, 15880C>T, 16030A>T, 16070G>A, 16171A>G, 26465T>A, 26489T>A, 26492T>C, 26681C>T, 26696A>T, 26852A>G, 26864C>T, 26914C>T, 27016G>A, 27040G>T, 27064T>C, 27085T>C, 27571A>G, 28586T>A, 28745T>A, 28929A>G, 29021A>G, 29267T>C, 29297T>C, 29545C>T, 29568G>A, 29849G>A, 29852T>C, 29861A>G, 29909C>T, 29954C>T, 30187G>A, 30229A>T, 30244G>T, 30288T>C, 30586T>C, 31160C>G, 31404A>C, 31415A>T, 31446A>T, 31479G>A, 31545G>A, 32018C>A, 32057T>C, 32069G>T, 32075G>T, 32086T>C, 32142G>A, 32209C>T, 32212T>G, 32215T>G, 32389T>G, 33908T>G, 33946A>T, 33950G>T, 34046T>C, 34097C>T, 34148A>G, 34229A>G, 34271C>G, 35312C>T, 35447A>T, 35565A>G, 35629T>G, 35824A>G
CDS
4816569.7%74895.2%115 (100%)113 (98.3%)0/0/0/00
14257844.6%177598.7%258 (100%)257 (99.6%)0/0/0/01
1841486.2%239098.3%357 (100%)354 (99.2%)0/0/0/01
Protein mutations:P152S (2939C>T)
Codon mutations:CCG152TCG (2939C>T), GAT153GAC (2944T>C), GGA174GGT (3007A>T), GCG191GCA (3058G>A), GCA192GCT (3061A>T), GGC205GGT (3100C>T), GGC238GGT (3199C>T), ATC358ATT (3559C>T), CCG376CCC (3613G>C), GGT380GGG (3625T>G)
122196.5%1456100%221 (100%)221 (100%)0/0/0/00
339196.8%251099.5%389 (100%)388 (99.7%)0/0/0/00
Protein mutations:V3G (4377T>G)
Codon mutations:GTT3GGT (4377T>G), AAG39AAA (4486G>A), TTA107TTG (4690A>G), ACG245ACT (5104G>T), ACA286ACT (5227A>T)
1108100%74998.4%108 (100%)106 (98.1%)0/0/0/01
Protein mutations:V20A (5885T>C), D64E (6018T>A)
Codon mutations:GTT20GCT (5885T>C), GAT64GAA (6018T>A)
16346.0%41492.8%63 (100%)59 (93.7%)0/0/0/00
Protein mutations:Q28L (6229A>T), P44L (6277C>T), V45I (6279G>A)
Codon mutations:CAG28CTG (6229A>T), CCG44CTG (6277C>T), GTT45ATT (6279G>A)
7418761.0%81197.5%114 (100%)112 (98.2%)0/0/0/01
Protein mutations:S137R (7460C>A), P172S (7563C>T)
Codon mutations:GCT99GCC (7346T>C), AGC137AGA (7460C>A), CCT172TCT (7563C>T)
441052.5%166298.3%262 (100%)257 (98.1%)0/0/0/00
Protein mutations:A201V (8374C>T), I266T (8569T>C), Q343K (8799C>A)
Codon mutations:GCG201GTG (8374C>T), GCG215GCT (8417G>T), ATC266ACC (8569T>C), GAT298GAC (8666T>C), ATT312ATC (8708T>C), CAG343AAG (8799C>A)
3111128.6%24190.9%34 (100%)33 (97.1%)0/0/0/00
12045945.5%131497.1%209 (100%)207 (99.0%)0/0/0/01
136096.4%242098.9%347 (100%)345 (99.4%)0/0/0/01
Protein mutations:T228S (14017C>G)
Codon mutations:GAC3GAT (13343C>T), AAT4AAC (13346T>C), CGA205CGG (13949A>G), GCC216GCT (13982C>T), ACC228AGC (14017C>G), CGG267CGA (14135G>A), TTT300TTC (14234T>C), GTT313GTC (14273T>C), CCG333CCA (14333G>A)
118395.6%112697.7%175 (100%)172 (98.3%)0/0/0/01
Protein mutations:R2S (14419G>T), I45V (14546A>G)
Codon mutations:AGG2AGT (14419G>T), ATT45GTT (14546A>G), GGC70GGT (14623C>T)
114221.8%21898.2%31 (100%)31 (100%)0/0/0/01
135375.6%183497.6%267 (100%)260 (97.4%)0/0/0/01
Protein mutations:I55V (15536A>G), T127A (15752A>G), G233S (16070G>A)
Codon mutations:ATC55GTC (15536A>G), ACC127GCC (15752A>G), ACC169ACT (15880C>T), CGA219CGT (16030A>T), GGC233AGC (16070G>A), GTA266GTG (16171A>G)
119580.5%116298.1%157 (100%)154 (98.1%)0/0/0/01
110031.3%44498.0%68 (100%)67 (98.5%)0/0/0/00
110718.3%23194.3%32 (100%)31 (96.9%)0/0/0/00
127174.2%147098.5%201 (100%)199 (99.0%)0/0/0/01
34338811.9%310100%46 (100%)46 (100%)0/0/0/01
115574.9%93998.6%134 (100%)132 (98.5%)0/0/0/00
115456.0%102399.0%154 (100%)153 (99.4%)0/0/0/00
1227100%157999.4%227 (100%)226 (99.6%)0/0/0/01
Protein mutations:R226H (26864C>T)
Codon mutations:TCA152TCG (27085T>C), CCA159CCG (27064T>C), ATC167ATA (27040G>T), CGC175CGT (27016G>A), CAG209CAA (26914C>T), CGT226CAT (26864C>T)
17968.7%62599.4%79 (100%)78 (98.7%)0/0/0/00
1225100%162299.6%225 (100%)224 (99.6%)0/0/0/01
Protein mutations:I95T (28929A>G)
Codon mutations:GTT64GTC (29021A>G), ATA95ACA (28929A>G), CCA156CCT (28745T>A), GGA209GGT (28586T>A)
167100%434100%67 (100%)67 (100%)0/0/0/01
118493.5%119799.0%172 (100%)170 (98.8%)0/0/0/01
Protein mutations:V8I (29568G>A)
Codon mutations:GTA8ATA (29568G>A), CAG101CAA (29849G>A), CGT102CGC (29852T>C), GAA105GAG (29861A>G), ATC121ATT (29909C>T), GAC136GAT (29954C>T)
1113100%74299.2%113 (100%)112 (99.1%)0/0/0/01
Protein mutations:I65T (30288T>C)
Codon mutations:GTG31GTA (30187G>A), GCA45GCT (30229A>T), GGG50GGT (30244G>T), ATC65ACC (30288T>C)
131475.5%168198.1%237 (100%)235 (99.2%)0/0/0/01
Protein mutations:R240G (31160C>G)
Codon mutations:CGT48CGC (30586T>C), CGT240GGT (31160C>G)
116387.3%100298.2%144 (100%)142 (98.6%)0/0/0/00
Protein mutations:E8D (31404A>C), Y12F (31415A>T)
Codon mutations:GAA8GAC (31404A>C), TAC12TTC (31415A>T), GGA22GGT (31446A>T), CGG33CGA (31479G>A), GGG55GGA (31545G>A)
1109100%70098.9%109 (100%)107 (98.2%)0/0/0/01
Protein mutations:V71A (32086T>C), E90K (32142G>A)
Codon mutations:CGC48CGA (32018C>A), GGT61GGC (32057T>C), GGG65GGT (32069G>T), ACG67ACT (32075G>T), GTG71GCG (32086T>C), GAG90AAG (32142G>A)
17227236.0%66397.2%98 (100%)97 (99.0%)0/0/0/01
133099.4%241699.1%330 (100%)327 (99.1%)0/0/0/00
Protein mutations:Q125L (33946A>T), D233E (34271C>G)
Codon mutations:GCT112GCG (33908T>G), CAG125CTG (33946A>T), CTG126CTT (33950G>T), GAT158GAC (34046T>C), GAC175GAT (34097C>T), CCA192CCG (34148A>G), GCA219GCG (34229A>G), GAC233GAG (34271C>G)
1168100%119298.3%168 (100%)165 (98.2%)0/0/0/01
Protein mutations:S5C (35447A>T), D44G (35565A>G), S65R (35629T>G)
Codon mutations:AGC5TGC (35447A>T), GAC44GGC (35565A>G), AGT65AGG (35629T>G), CTA130CTG (35824A>G)
1021097.3%50100%8 (100%)8 (100%)0/0/0/01
13731.6%29498.7%37 (100%)36 (97.3%)0/0/0/00
Proteins
4816569.7%74895.2%115 (100%)113 (98.3%)0/0/0/00
Protein mutations:none
Codon mutations:none
14257844.6%177598.7%258 (100%)257 (99.6%)0/0/0/01
Protein mutations:none
Codon mutations:AAG533AAA (2157G>A), CTG558TTG (2230C>T), TAT572TAC (2274T>C)
1841486.2%239098.3%357 (100%)354 (99.2%)0/0/0/01
Protein mutations:P152S (2939C>T)
Codon mutations:CCG152TCG (2939C>T), GAT153GAC (2944T>C), GGA174GGT (3007A>T), GCG191GCA (3058G>A), GCA192GCT (3061A>T), GGC205GGT (3100C>T), GGC238GGT (3199C>T), ATC358ATT (3559C>T), CCG376CCC (3613G>C), GGT380GGG (3625T>G)
122196.5%1456100%221 (100%)221 (100%)0/0/0/00
Protein mutations:none
Codon mutations:none
339196.8%251099.5%389 (100%)388 (99.7%)0/0/0/00
Protein mutations:V3G (4377T>G)
Codon mutations:GTT3GGT (4377T>G), AAG39AAA (4486G>A), TTA107TTG (4690A>G), ACG245ACT (5104G>T), ACA286ACT (5227A>T)
1108100%74998.4%108 (100%)106 (98.1%)0/0/0/01
Protein mutations:V20A (5885T>C), D64E (6018T>A)
Codon mutations:GTT20GCT (5885T>C), GAT64GAA (6018T>A)
16346.0%41492.8%63 (100%)59 (93.7%)0/0/0/00
Protein mutations:Q28L (6229A>T), P44L (6277C>T), V45I (6279G>A)
Codon mutations:CAG28CTG (6229A>T), CCG44CTG (6277C>T), GTT45ATT (6279G>A)
7418761.0%81197.5%114 (100%)112 (98.2%)0/0/0/01
Protein mutations:S137R (7460C>A), P172S (7563C>T)
Codon mutations:GCT99GCC (7346T>C), AGC137AGA (7460C>A), CCT172TCT (7563C>T)
441052.5%166298.3%262 (100%)257 (98.1%)0/0/0/00
Protein mutations:A201V (8374C>T), I266T (8569T>C), Q343K (8799C>A)
Codon mutations:GCG201GTG (8374C>T), GCG215GCT (8417G>T), ATC266ACC (8569T>C), GAT298GAC (8666T>C), ATT312ATC (8708T>C), CAG343AAG (8799C>A)
3111128.6%24190.9%34 (100%)33 (97.1%)0/0/0/00
Protein mutations:none
Codon mutations:none
12045945.5%131497.1%209 (100%)207 (99.0%)0/0/0/01
Protein mutations:none
Codon mutations:none
136096.4%242098.9%347 (100%)345 (99.4%)0/0/0/01
Protein mutations:T228S (14017C>G)
Codon mutations:GAC3GAT (13343C>T), AAT4AAC (13346T>C), CGA205CGG (13949A>G), GCC216GCT (13982C>T), ACC228AGC (14017C>G), CGG267CGA (14135G>A), TTT300TTC (14234T>C), GTT313GTC (14273T>C), CCG333CCA (14333G>A)
118395.6%112697.7%175 (100%)172 (98.3%)0/0/0/01
Protein mutations:R2S (14419G>T), I45V (14546A>G)
Codon mutations:AGG2AGT (14419G>T), ATT45GTT (14546A>G), GGC70GGT (14623C>T)
114221.8%21898.2%31 (100%)31 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
135375.6%183497.6%267 (100%)260 (97.4%)0/0/0/01
Protein mutations:I55V (15536A>G), T127A (15752A>G), G233S (16070G>A)
Codon mutations:ATC55GTC (15536A>G), ACC127GCC (15752A>G), ACC169ACT (15880C>T), CGA219CGT (16030A>T), GGC233AGC (16070G>A), GTA266GTG (16171A>G)
119580.5%116298.1%157 (100%)154 (98.1%)0/0/0/01
Protein mutations:none
Codon mutations:none
110031.3%44498.0%68 (100%)67 (98.5%)0/0/0/00
Protein mutations:none
Codon mutations:none
110718.3%23194.3%32 (100%)31 (96.9%)0/0/0/00
Protein mutations:none
Codon mutations:none
127174.2%147098.5%201 (100%)199 (99.0%)0/0/0/01
Protein mutations:none
Codon mutations:none
34338811.9%310100%46 (100%)46 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
115574.9%93998.6%134 (100%)132 (98.5%)0/0/0/00
Protein mutations:none
Codon mutations:none
115456.0%102399.0%154 (100%)153 (99.4%)0/0/0/00
Protein mutations:none
Codon mutations:GCT33GCA (26696A>T), GAG38GAA (26681C>T), GAA101GAG (26492T>C), CCA102CCT (26489T>A), ACA110ACT (26465T>A)
1227100%157999.4%227 (100%)226 (99.6%)0/0/0/01
Protein mutations:R226H (26864C>T)
Codon mutations:TCA152TCG (27085T>C), CCA159CCG (27064T>C), ATC167ATA (27040G>T), CGC175CGT (27016G>A), CAG209CAA (26914C>T), CGT226CAT (26864C>T)
17968.7%62599.4%79 (100%)78 (98.7%)0/0/0/00
Protein mutations:none
Codon mutations:TTA48TTG (27571A>G)
1225100%162299.6%225 (100%)224 (99.6%)0/0/0/01
Protein mutations:I95T (28929A>G)
Codon mutations:GTT64GTC (29021A>G), ATA95ACA (28929A>G), CCA156CCT (28745T>A), GGA209GGT (28586T>A)
167100%434100%67 (100%)67 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
118493.5%119799.0%172 (100%)170 (98.8%)0/0/0/01
Protein mutations:V8I (29568G>A)
Codon mutations:GTA8ATA (29568G>A), CAG101CAA (29849G>A), CGT102CGC (29852T>C), GAA105GAG (29861A>G), ATC121ATT (29909C>T), GAC136GAT (29954C>T)
1113100%74299.2%113 (100%)112 (99.1%)0/0/0/01
Protein mutations:I65T (30288T>C)
Codon mutations:GTG31GTA (30187G>A), GCA45GCT (30229A>T), GGG50GGT (30244G>T), ATC65ACC (30288T>C)
131475.5%168198.1%237 (100%)235 (99.2%)0/0/0/01
Protein mutations:R240G (31160C>G)
Codon mutations:CGT48CGC (30586T>C), CGT240GGT (31160C>G)
116387.3%100298.2%144 (100%)142 (98.6%)0/0/0/00
Protein mutations:E8D (31404A>C), Y12F (31415A>T)
Codon mutations:GAA8GAC (31404A>C), TAC12TTC (31415A>T), GGA22GGT (31446A>T), CGG33CGA (31479G>A), GGG55GGA (31545G>A)
1109100%70098.9%109 (100%)107 (98.2%)0/0/0/01
Protein mutations:V71A (32086T>C), E90K (32142G>A)
Codon mutations:CGC48CGA (32018C>A), GGT61GGC (32057T>C), GGG65GGT (32069G>T), ACG67ACT (32075G>T), GTG71GCG (32086T>C), GAG90AAG (32142G>A)
17227236.0%66397.2%98 (100%)97 (99.0%)0/0/0/01
Protein mutations:none
Codon mutations:none
133099.4%241699.1%330 (100%)327 (99.1%)0/0/0/00
Protein mutations:Q125L (33946A>T), D233E (34271C>G)
Codon mutations:GCT112GCG (33908T>G), CAG125CTG (33946A>T), CTG126CTT (33950G>T), GAT158GAC (34046T>C), GAC175GAT (34097C>T), CCA192CCG (34148A>G), GCA219GCG (34229A>G), GAC233GAG (34271C>G)
1168100%119298.3%168 (100%)165 (98.2%)0/0/0/01
Protein mutations:S5C (35447A>T), D44G (35565A>G), S65R (35629T>G)
Codon mutations:AGC5TGC (35447A>T), GAC44GGC (35565A>G), AGT65AGG (35629T>G), CTA130CTG (35824A>G)
1021097.3%50100%8 (100%)8 (100%)0/0/0/01
Protein mutations:none
Codon mutations:none
13731.6%29498.7%37 (100%)36 (97.3%)0/0/0/00
Protein mutations:none
Codon mutations:none
*: Inserts / Deletes / Misaligned / Frameshifts

Analysis details

This analysis was performed with panviral2.43