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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
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%
| 40.5
/ NA
| 13 | G140G (GGA→GGG) | wzx | O16 family O‑antigen flippase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/6); total (7/6) |
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC > NZ_CP009273/2102560‑2102732
|
tttGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTcccc < 1:34282/90‑1 (MQ=255)
cacaAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAg > 2:315163/1‑90 (MQ=255)
acaAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGc < 1:301294/90‑1 (MQ=255)
aataaatGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGAt < 2:185245/90‑1 (MQ=255)
tAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGAt > 2:466759/1‑90 (MQ=255)
ataataGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTc > 2:294943/1‑90 (MQ=255)
ccAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTa < 2:42030/90‑1 (MQ=255)
tactTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGAcc > 1:240523/1‑90 (MQ=255)
actTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCa > 2:167538/1‑90 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:126548/1‑90 (MQ=255)
aGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACg > 2:370824/1‑90 (MQ=255)
atttcatttTTTCTTTCCCCTGAAGCAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCAt < 1:443764/90‑1 (MQ=255)
tcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCt < 1:191370/90‑1 (MQ=255)
tcatttTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCt < 2:420771/90‑1 (MQ=255)
tttccCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTc < 2:150531/90‑1 (MQ=255)
|
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC > NZ_CP009273/2102560‑2102732
|
| 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
CTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC > NZ_CP009273/2102555‑2102732
|
CTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAA < SRR3722087.300010/100‑1 (MQ=60)
TTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCC < SRR3722087.34558/100‑1 (MQ=60)
ACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGT < SRR3722087.304417/100‑1 (MQ=60)
GATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACC > SRR3722087.242798/1‑100 (MQ=60)
ATTTCATTTTTTCTTTCCCCTGAAGCAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATA < SRR3722087.448954/100‑1 (MQ=60)
TCATTTTTTCTTTCCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC < SRR3722087.193055/100‑1 (MQ=60)
|
CTGACTTTGTGTTCACAAAAATAAATGTTAGAGGGATAATAGCCAAGCGGGATAAAATACTACTTAAAGTCAGCCATTTCATTTTTTCTTTTCCCTGAAACAGCCAGATAGGGTAGATTAAATTCCCGACTAATGCAGGAACAAACGACCATATAATTACGGCATGCTTGTTATATTC > NZ_CP009273/2102555‑2102732
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
