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 |
1,562,111 |
A→C |
68.8% |
I706I (ATA→ATC) |
evgS → |
hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,562,111 | 0 | A | C | 68.8%
| 79.7
/ 37.0
| 64 | I706I (ATA→ATC) | evgS | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| Reads supporting (aligned to +/- strand): ref base A (15/5); new base C (21/23); total (36/28) |
| Fisher's exact test for biased strand distribution p-value = 5.79e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.15e-01 |
TGGCAAGATATTACTGAAACGCGTGATCTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGATGAGTCACGAAATAAGAAC > minE/1562046‑1562167
|
tGGCAAGATATTACTGAAACGCGTGATCTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAg < 1:1849367/69‑1 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:37567/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:1971997/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:2084318/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:2098117/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:2208711/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:2756423/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:2922008/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:3342454/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:2494121/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:380046/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:441445/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:45902/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:698195/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:849487/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:945701/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:977410/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:1819090/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:1834511/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:114710/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:1350440/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:1325865/69‑3 (MQ=255)
atatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:1676614/69‑3 (MQ=255)
tatTACCGAGACGCGTGATTTAATTCATGCACTCGAAGTAGAGAGAAATAAAGCGATCAATGCAActg < 1:3155203/68‑3 (MQ=255)
cTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCt > 1:1192632/1‑68 (MQ=255)
cTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCt > 1:658483/1‑68 (MQ=255)
cTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCt > 1:2178050/1‑68 (MQ=255)
cTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCt > 1:1377843/1‑68 (MQ=255)
cTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCt > 1:2535064/1‑68 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:3048387/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:1665204/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:1237235/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:459691/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:225596/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:2201734/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:2197818/1‑69 (MQ=255)
taatGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAAc > 1:74167/1‑69 (MQ=255)
aatGCACTAGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGATTCTGGCAAc > 1:461201/1‑68 (MQ=255)
tGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGa < 1:1157624/68‑1 (MQ=255)
tGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGa < 1:1036409/68‑1 (MQ=255)
tGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGa < 1:2584063/68‑1 (MQ=255)
gAGGTAGAAAAATATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGATGAGTCa > 1:1993970/1‑68 (MQ=255)
aaaaaaTAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGATGAGTCACGAAATAAg < 1:2712530/69‑1 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAAt > 1:2989771/1‑63 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGaa > 1:1215069/1‑68 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGa > 1:2417020/1‑67 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:1866465/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:2957481/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:1760338/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:804430/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:1696350/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:1684729/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:2099413/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:533365/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:2193892/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:1002794/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:410046/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:2619377/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:356847/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:33651/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:3205664/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:3157993/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGCCAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:2834469/1‑69 (MQ=255)
aaaTAAAGCGATCAATGCAACTGTCGCAAAAAGACAGTTTCTGGCAACAATGAGTCACGAAATAAGAac > 1:140822/1‑69 (MQ=255)
|
TGGCAAGATATTACTGAAACGCGTGATCTAATTAATGCACTCGAGGTAGAAAAAAATAAAGCGATAAAGGCTACCGTAGCAAAAAGTCAGTTTCTGGCAACGATGAGTCACGAAATAAGAAC > minE/1562046‑1562167
|
| 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
