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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,102,646 |
T→C |
G140G (GGA→GGG) |
wzx ← |
O16 family O‑antigen flippase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,102,646 | 0 | T | C | 100.0%
| 70.5
/ NA
| 22 | G140G (GGA→GGG) | wzx | O16 family O‑antigen flippase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/13); total (9/13) |
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA > NZ_CP009273/2102560‑2102727
|
tttGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTcccc < 1:320646/90‑1 (MQ=255)
gtgtTCACAGAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGa > 1:307836/1‑90 (MQ=255)
gtgtTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGa > 1:391556/1‑90 (MQ=255)
tgtTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGaa < 2:374374/90‑1 (MQ=255)
aataaatGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt < 1:87382/90‑1 (MQ=255)
taaatGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAg < 2:297331/90‑1 (MQ=255)
gATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt > 2:406520/1‑75 (MQ=255)
gATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt < 1:406520/75‑1 (MQ=255)
gATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAAtt > 2:255481/1‑90 (MQ=255)
gCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGc < 2:342671/90‑1 (MQ=255)
gATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGa < 2:135866/90‑1 (MQ=255)
aTACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAAc < 1:224803/90‑1 (MQ=255)
aTACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAAc < 2:91376/90‑1 (MQ=255)
ctTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCat < 2:272214/90‑1 (MQ=255)
ctTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCat < 1:386524/90‑1 (MQ=255)
ctTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCat < 1:370036/90‑1 (MQ=255)
tAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCatat > 2:185042/1‑90 (MQ=255)
gTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAAtt < 1:30780/90‑1 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:105683/1‑90 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:282297/1‑90 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:283376/1‑90 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 1:129351/1‑90 (MQ=255)
ttttttCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGt < 1:255481/90‑1 (MQ=255)
ttttctttccCCTGAAACAGCCAGGTAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTta < 2:307836/90‑1 (MQ=255)
ttttctttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTta < 2:129351/90‑1 (MQ=255)
|
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTA > NZ_CP009273/2102560‑2102727
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAACAAGCA > NZ_CP009273/2102553‑2102743
|
ATCTGACTTTGTGTTCACAGAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGA > SRR3722091.313083/1‑100 (MQ=60)
ATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGA > SRR3722091.398458/1‑100 (MQ=60)
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCC < SRR3722091.326182/100‑1 (MQ=60)
gacagATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATT < SRR3722091.413655/95‑1 (MQ=60)
AATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATT < SRR3722091.88727/100‑1 (MQ=60)
ATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAA < SRR3722091.228270/100‑1 (MQ=60)
ACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACG > SRR3722091.131300/1‑100 (MQ=60)
CTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGG < SRR3722091.376571/100‑1 (MQ=60)
CTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGG < SRR3722091.393346/100‑1 (MQ=60)
GTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCT < SRR3722091.31212/100‑1 (MQ=60)
TTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGG < SRR3722091.259565/100‑1 (MQ=60)
TTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAACAAGCA < SRR3722091.107305/100‑1 (MQ=60)
|
ATCTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTCAGGAACAAGCA > NZ_CP009273/2102553‑2102743
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
