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 |
1,268,191 |
C→T |
52.4% |
L138L (TTG→TTA) |
pgsA ← |
phosphatidylglycerophosphate synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,268,191 | 0 | C | T | 52.4%
| 1.8
/ 74.8
| 84 | L138L (TTG→TTA) | pgsA | phosphatidylglycerophosphate synthetase |
| Reads supporting (aligned to +/- strand): ref base C (36/4); new base T (32/12); total (68/16) |
| Fisher's exact test for biased strand distribution p-value = 5.45e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.32e-01 |
GCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCGTTTA > minE/1268126‑1268257
|
gCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAAc < 1:370670/69‑1 (MQ=255)
aagaagAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:1393411/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:3175254/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:812970/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:756212/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:2602654/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:1634636/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:1243722/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:1337783/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:1461076/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:453783/1‑69 (MQ=255)
aaGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacc > 1:1551607/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:3309944/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:3357684/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:3000442/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:343754/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:2203007/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:2903608/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:2629523/1‑69 (MQ=255)
cAATACCGGCGTACTCAACCCAAATGTTCGGACCCCACAGCAGCCATGCCAACGCCACCATCTGGGCAg > 1:1676471/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:2207105/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:2920648/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:2694483/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:2594632/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:857167/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:1834352/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:470502/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGtt > 1:471524/1‑69 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGt > 1:2350496/1‑68 (MQ=255)
ccGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGt > 1:578630/1‑68 (MQ=255)
ccGGCGTACTCAACCCAAATGTTAGGACGCCGCAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGt > 1:464065/1‑68 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGTTTTTCACttt > 1:1389678/1‑69 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACttt > 1:3395194/1‑69 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACttt > 1:2962497/1‑69 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACttt > 1:1664920/1‑69 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACttt > 1:45516/1‑69 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACttt > 1:2347407/1‑69 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGccacca > 1:1069198/1‑47 (MQ=39)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGc > 1:470161/1‑54 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGc > 1:2992945/1‑54 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:910723/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:359364/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:15233/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:1676622/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:3372684/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:1811507/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:1890306/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:1202202/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:2966251/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:1183374/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:591875/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:2486107/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:2400996/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:874526/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:2681795/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:107491/1‑55 (MQ=255)
cTCAACCCAAATGTTCGGACGCCACAGCAGCCAGCCTAACGCCACCATCTgg > 1:3206286/1‑52 (MQ=255)
cTCAACCCAAATGTTAGGACGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCa > 1:1310950/1‑55 (MQ=255)
cGGACGCCATAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:2851054/1‑69 (MQ=255)
cGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:1586206/1‑69 (MQ=255)
cGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:585792/1‑69 (MQ=255)
cGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:1107532/1‑69 (MQ=255)
cGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:1897691/1‑69 (MQ=255)
cGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:2131043/1‑69 (MQ=255)
cGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGAc > 1:21420/1‑69 (MQ=255)
cGCCACAGCAGCCAGGCTTACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:1237328/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:1036112/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:3336816/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:1634229/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:2411797/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:2390480/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:3238690/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:2162867/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:2338734/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:426156/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATc < 1:230622/57‑1 (MQ=255)
cGCCACAGCAGCCAGGCTAACGCCACCATCTGGGCAGTGGTTCTCACTTTCCCAATc < 1:3243663/57‑1 (MQ=255)
agcCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACt > 1:2847506/1‑68 (MQ=255)
agcCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTg > 1:1135422/1‑69 (MQ=255)
agcCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTg > 1:2222606/1‑69 (MQ=255)
cATGCCAACGCCACCATCTGGGCAGTTGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCg > 1:565634/1‑68 (MQ=255)
aTGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCGtt < 1:2626592/69‑1 (MQ=255)
tGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCGtt < 1:809355/68‑1 (MQ=255)
tGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCGtt < 1:3316855/68‑1 (MQ=255)
ccAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCGTTTa > 1:2455692/1‑68 (MQ=255)
|
GCCACAAAGAAAAGTGCAATACCGGCGTACTCAACCCAAATGTTCGGACGCCACAGCAGCCATGCCAACGCCACCATCTGGGCAGTGGTTTTCACTTTCCCAATCCAGGAGACGGCCACGCTACTGCGTTTA > minE/1268126‑1268257
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
