Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,670,359 |
T→C |
G454G (GGA→GGG) |
yphE ← |
sugar ABC transporter ATP‑binding protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,670,359 | 0 | T | C | 100.0%
| 130.9
/ NA
| 37 | G454G (GGA→GGG) | yphE | sugar ABC transporter ATP‑binding protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (21/16); total (21/16) |
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > NZ_CP009273/2670283‑2670440
|
cgtgcTGTAATAACAGGATGCGGTCACACCCCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca < 1:173028/90‑1 (MQ=255)
gcTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCt > 1:739680/1‑90 (MQ=255)
tGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCa < 1:642509/90‑1 (MQ=255)
aataaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 1:89622/90‑1 (MQ=255)
aataaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg > 2:36725/1‑90 (MQ=255)
aataaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 2:559663/90‑1 (MQ=255)
aataaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 1:557583/90‑1 (MQ=255)
aataaCAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGAAGCCAGCTCACgg > 1:546839/1‑90 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCGCTTAAGTGAAGATAAACACCACGCTTTTCCCTTCGGCAGACAGCTCACGGACAAttca > 1:238512/1‑87 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca > 1:485001/1‑74 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca < 2:485001/74‑1 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 1:508650/82‑1 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg > 2:508650/1‑82 (MQ=255)
gATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACg > 1:277518/1‑90 (MQ=255)
ggTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTaaa > 1:57887/1‑90 (MQ=255)
ggTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTaaa < 2:550711/90‑1 (MQ=255)
cacacaCCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATct < 2:277518/90‑1 (MQ=255)
cAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGttt < 2:496890/90‑1 (MQ=255)
aaCTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca > 1:686228/1‑52 (MQ=255)
aaCTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGcagcca < 2:686228/52‑1 (MQ=255)
cTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGAcgc > 2:667125/1‑90 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg > 1:187266/1‑48 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 2:328520/48‑1 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg < 2:187266/48‑1 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACgg > 1:328520/1‑48 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATctgc < 1:661163/66‑1 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATctgc > 2:661163/1‑66 (MQ=255)
tCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGAcgccg > 2:63603/1‑90 (MQ=255)
aCTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCcgcg > 1:45192/1‑90 (MQ=255)
cTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCcgcgc > 1:768454/1‑90 (MQ=255)
ggAGATAAACACCACGCTTTTCCCTTCGGcagcca > 2:22538/1‑35 (MQ=38)
ggAGATAAACACCACGCTTTTCCCTTCGGcagcca < 1:22538/35‑1 (MQ=38)
aaaCACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCtc < 1:702958/90‑1 (MQ=255)
accacGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCtcgtcg > 1:643392/1‑90 (MQ=255)
ccacGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGa > 2:397914/1‑90 (MQ=255)
cacGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAg > 2:424675/1‑90 (MQ=255)
acGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCCTCGATATCGACGCCGCGCGTTGGCTCGTCGAGc > 1:753311/1‑90 (MQ=255)
|
CGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > NZ_CP009273/2670283‑2670440
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATCTG > NZ_CP009273/2670276‑2670451
|
AACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCT > SRR3722073.754661/1‑100 (MQ=60)
GCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGAAGCCAGCTCACGG > SRR3722073.558262/1‑100 (MQ=60)
acacactgcatatcgtcggcagcgtcagatgtgtataagagacagCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGAC < SRR3722073.23107/55‑1 (MQ=60)
CGTGCTGTAATAACAGGATGCGGTCACACCCCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGAC < SRR3722073.176407/100‑1 (MQ=60)
TGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATAC < SRR3722073.655760/100‑1 (MQ=60)
GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACctgtct > SRR3722073.495305/1‑94 (MQ=60)
GTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACG > SRR3722073.283393/1‑100 (MQ=60)
GTAATAAAAGGATGCGGTCACACACCAGCGGCAACTCCTCCGCTTAAGTGAAGATAAACACCACGCTTTTCCCTTCGGCAGACAGCTCACGGACAATtca > SRR3722073.243508/1‑97 (MQ=60)
AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT < SRR3722073.91629/100‑1 (MQ=60)
AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT < SRR3722073.519380/100‑1 (MQ=60)
AATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGT < SRR3722073.569223/100‑1 (MQ=60)
AACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAA > SRR3722073.59253/1‑100 (MQ=60)
tgtataagagacagCTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTT < SRR3722073.674716/86‑1 (MQ=60)
CACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACctgtctcttatacacatctgacgctgcc > SRR3722073.700210/1‑72 (MQ=60)
CTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTctgtctcttatacacatctgacgctgccgacg > SRR3722073.335494/1‑68 (MQ=60)
CTCCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTctgtctcttatacacatctgacgctgccgacg > SRR3722073.190944/1‑68 (MQ=60)
CCTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCG > SRR3722073.46270/1‑100 (MQ=60)
CTCCACTTCACTGGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGC > SRR3722073.783973/1‑100 (MQ=60)
GGAGATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCG > SRR3722073.656658/1‑100 (MQ=60)
GATAAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCCTCGATATCGACGCCGCGCGTTGGCTCGTCGAGC > SRR3722073.768557/1‑100 (MQ=60)
AAACACCACGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAAC < SRR3722073.717202/100‑1 (MQ=60)
CGCTTTTCCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATCTG > SRR3722073.652029/1‑100 (MQ=60)
|
AACGTGCCGTGCTGTAATAACAGGATGCGGTCACACACCAGCGGCAACTCCTCCACTTCACTGGAGATAAACACCACGCTTTTTCCTTCGGCAGCCAGCTCACGGACAATACGGTAAATCTGCTGTTTGGCTTCGATATCGACGCCGCGCGTTGGCTCGTCGAGCAACAAAATCTG > NZ_CP009273/2670276‑2670451
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
