Version 2.22.2
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