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 |
1,448,026 |
A→G |
50.0% |
L144L (TTA→TTG) |
atoS → |
sensory histidine kinase in two‑component regulatory system with AtoC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,448,026 | 0 | A | G | 50.0%
| ‑4.2
/ 59.4
| 66 | L144L (TTA→TTG) | atoS | sensory histidine kinase in two‑component regulatory system with AtoC |
| Reads supporting (aligned to +/- strand): ref base A (17/16); new base G (23/10); total (40/26) |
| Fisher's exact test for biased strand distribution p-value = 2.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
AATGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTG > minE/1447961‑1448081
|
aatGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGtt < 1:3019717/69‑1 (MQ=255)
aatGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGtt < 1:3342928/69‑1 (MQ=255)
aatGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGtt < 1:1380926/69‑1 (MQ=255)
atGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGttt > 1:2922666/1‑69 (MQ=255)
atGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGttt > 1:2793410/1‑69 (MQ=255)
aCCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTcaggca > 1:1980572/1‑67 (MQ=255)
aCCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTcaggca > 1:2189962/1‑67 (MQ=255)
aCCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTcaggca > 1:3228305/1‑67 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:888163/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:2751140/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:247958/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:2423988/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:795925/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:1187411/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:2012068/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:1912230/69‑1 (MQ=255)
cAGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGAAGGTGcgcg < 1:738754/69‑1 (MQ=255)
aGATCACCCTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGcgcg < 1:3196113/68‑1 (MQ=255)
tCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGa < 1:1431051/69‑1 (MQ=255)
tCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGa < 1:1553962/69‑1 (MQ=255)
tCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGa < 1:2045655/69‑1 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTcag > 1:2146092/1‑47 (MQ=39)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:1437915/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:447125/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:2948528/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:458754/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:425732/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:917085/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:2724978/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:6941/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:1388857/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:337266/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:2409446/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:706705/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:1482120/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:228005/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:149379/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:1279222/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:1516086/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:1680629/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGatat > 1:123288/1‑69 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGata > 1:1508011/1‑68 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGata > 1:649477/1‑68 (MQ=255)
cccTGGTCGCGAAGTCATGCGTACAAATACCCCTTTGGTTTATTCAGGCAGGCAGGTGCGCGGCGata > 1:1076057/1‑68 (MQ=255)
gAAGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTc < 1:2709577/68‑1 (MQ=255)
aaGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGGGCGCGGCGATATTTTGAATTc < 1:1674981/67‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:3128845/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:2093700/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:2890931/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:1967740/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:1961792/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:1250159/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:970463/69‑1 (MQ=255)
aTGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTc < 1:99355/69‑1 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATg > 1:2333248/1‑59 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCAtt > 1:1124940/1‑68 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:1012709/1‑69 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:716281/1‑69 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:2310793/1‑69 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:2273986/1‑69 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:1275324/1‑69 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:1042739/1‑69 (MQ=255)
cAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCCCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:1315936/1‑69 (MQ=255)
cAAATACCACTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:2653326/1‑69 (MQ=255)
cAAATACCACTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTg > 1:2649204/1‑69 (MQ=255)
tAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTccc > 1:281947/1‑52 (MQ=255)
|
AATGTCGGCGTTACCATTGCCGCAGATCACCCTGGTCGCGAAGTGATGCGTACAAATACCCCTTTAGTTTATTCAGGCAGGCAGGTGCGCGGCGATATTTTGAATTCAATGCTCCCCATTG > minE/1447961‑1448081
|
| 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
