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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,063,766 |
T→C |
29.9% |
intergenic (+116/+46) |
sodB → / ← ydhP |
superoxide dismutase, Fe/predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,063,766 | 0 | T | C | 29.9%
| 52.3
/ 26.2
| 60 | intergenic (+116/+46) | sodB/ydhP | superoxide dismutase, Fe/predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (3/39); new base C (13/5); total (16/44) |
| Fisher's exact test for biased strand distribution p-value = 6.75e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01 |
CGCGGATCATCGATGTAGGTCGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCA > minE/1063702‑1063829
|
cgcgGATCATCGATGTAGGTCGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAg > 1:364092/1‑68 (MQ=255)
cgcgGATCATCGATGTAGGTCGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGc > 1:941024/1‑69 (MQ=255)
tcatcGATGTAGGTCGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGt < 1:951087/69‑1 (MQ=255)
tcatcGATGTAGGTCGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGt < 1:1328545/69‑1 (MQ=255)
cGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTa < 1:1981736/69‑1 (MQ=255)
cGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTa < 1:2039752/69‑1 (MQ=255)
cGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTa < 1:171389/69‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTa < 1:1267247/68‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTa < 1:360865/68‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTAt < 1:399875/69‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTAt < 1:1126948/69‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTAt < 1:2514655/69‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTAt < 1:2265313/69‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTAt < 1:207292/69‑1 (MQ=255)
ggATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTAt < 1:3337388/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:3049192/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:717757/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:2937708/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:2884673/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:502169/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:1962607/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:1121776/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:1839319/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:1522198/69‑1 (MQ=255)
aTAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATcc < 1:1755557/69‑1 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTg > 1:1964241/1‑58 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:675294/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:1251676/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:1368584/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:1428121/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:2932671/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:2907726/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:1798476/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:893414/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:2754507/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:2361115/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:2302072/1‑69 (MQ=255)
aGATAAATCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCt > 1:1873680/1‑69 (MQ=255)
gATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTg < 1:558457/69‑1 (MQ=255)
gATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTg < 1:3074871/69‑1 (MQ=255)
aaaTCGCACGTTGTCAGCAACTGTAACGCATAAGGTTATcc < 1:2712535/41‑1 (MQ=255)
aaTCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTa > 1:415826/1‑68 (MQ=255)
aTCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGc < 1:938373/69‑1 (MQ=255)
tCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGc < 1:1059437/68‑1 (MQ=255)
tCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGc < 1:731638/68‑1 (MQ=255)
tCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTGGc < 1:328514/68‑1 (MQ=255)
tCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTGGc < 1:3107070/68‑1 (MQ=255)
tCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTGGc < 1:762656/68‑1 (MQ=255)
tCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTGGc < 1:2785917/68‑1 (MQ=255)
tCGCACGTTGCCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTGGc < 1:503827/68‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:1101730/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:472456/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:3230744/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:3156818/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:2962558/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:2787503/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:1946971/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:154820/69‑1 (MQ=255)
cGTTGTCAGCAACTGTAACGCAGAAGGTTATCATTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:349105/69‑1 (MQ=255)
gTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCa < 1:2882164/68‑1 (MQ=255)
|
CGCGGATCATCGATGTAGGTCGGATAAGGCACTCGCCGCATCCGGCAAGATAAATCGCACGTTGTCAGCAACTGTAACGCAGAAGGTTATCCTTCTGCGTTTTTGTTTAATTAGCTGTTAGCAACGCA > minE/1063702‑1063829
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
