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 |
768,263 |
A→G |
71.8% |
L257L (TTG→CTG) |
phoQ ← |
sensory histidine kinase in two‑compoent regulatory system with PhoP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 768,263 | 0 | A | G | 71.8%
| 78.3
/ 29.5
| 74 | L257L (TTG→CTG) | phoQ | sensory histidine kinase in two‑compoent regulatory system with PhoP |
| Reads supporting (aligned to +/- strand): ref base A (19/2); new base G (36/17); total (55/19) |
| Fisher's exact test for biased strand distribution p-value = 7.43e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
CTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGA > minE/768199‑768316
|
cTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCgg < 1:580871/69‑1 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:2791090/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1113015/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1154012/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1728029/1‑69 (MQ=255)
tGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTc > 1:1907952/1‑69 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:1529335/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:418225/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:388377/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:2335636/1‑68 (MQ=255)
cGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGt > 1:1280788/1‑68 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3025811/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:32631/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3021683/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3400868/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1741757/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:2967579/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:290117/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:2780576/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1501092/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1324565/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1377229/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1398755/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1399689/69‑1 (MQ=255)
gtcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:440871/69‑1 (MQ=255)
atcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:3274733/68‑1 (MQ=255)
tcgtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1015313/68‑1 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:1931800/1‑69 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:2236270/1‑69 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:2840487/1‑69 (MQ=255)
gtACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTc > 1:852748/1‑69 (MQ=255)
gtACGATATTTGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg < 1:1324081/66‑1 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGTTTCAGGTTTCGTACCAGACTGGTCAGt > 1:98501/1‑62 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGt > 1:1950816/1‑36 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTtctc > 1:1679537/1‑66 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:1081556/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:397703/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:2986230/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:766349/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:648456/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:505916/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:185105/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:1132697/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:1230448/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:1462000/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:1712164/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:1991686/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:24105/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:2478364/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:2448549/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:2531815/1‑69 (MQ=255)
tGTCGTAACGTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgc > 1:1824464/1‑68 (MQ=255)
tGTCGTAACCTTCGCGTTCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTcgcg > 1:27548/1‑69 (MQ=255)
aCGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGc > 1:2748588/1‑69 (MQ=255)
aCGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGc > 1:1315496/1‑69 (MQ=255)
aCGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGc > 1:134558/1‑69 (MQ=255)
aCGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGc > 1:1765725/1‑69 (MQ=255)
aCGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGc > 1:303136/1‑69 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:554095/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:2298775/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:806/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:1294863/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:696679/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:692806/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:2484845/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:339250/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:2823043/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:1481504/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:1983674/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:3291783/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:3389449/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:386707/1‑40 (MQ=255)
ttCACTTTTTAACAGTCGGTTCAGGTTTCGTACCAGACTg > 1:3401037/1‑40 (MQ=255)
aaCAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGa < 1:2713811/58‑1 (MQ=255)
|
CTATGGGTCAGGTCGGTGAGCGTCGTACGGTATTTGTCGTAACGTTCGCGTTCACTTTTTAACAATCGGTTCAGGTTTCGTACCAGACTGGTCAGTTCTCGCGTTGTGGCTGGATTGA > minE/768199‑768316
|
| 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
