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 |
2,517,413 |
G→A |
54.0% |
S554S (AGC→AGT) |
spoT ← |
bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,517,413 | 0 | G | A | 54.0%
| 5.6
/ 61.8
| 74 | S554S (AGC→AGT) | spoT | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| Reads supporting (aligned to +/- strand): ref base G (19/15); new base A (30/10); total (49/25) |
| Fisher's exact test for biased strand distribution p-value = 9.23e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.52e-01 |
GGGCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTCGCGACC > minE/2517348‑2517467
|
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:1012069/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:2544599/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:2661301/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:3086987/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:3288902/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:3325711/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:599380/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCtt > 1:106636/1‑69 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTAAATGGGCAGATGTCCGTGGCt > 1:2951968/1‑68 (MQ=255)
gggCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACC‑TTAATGGGCAGATGTCCGTGGCttt > 1:1920162/1‑69 (MQ=255)
cggcAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTgg < 1:716167/69‑1 (MQ=255)
cggcAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTgg < 1:793647/69‑1 (MQ=255)
caTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTg > 1:3336207/1‑67 (MQ=255)
caTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGcc > 1:3401967/1‑69 (MQ=255)
caTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGcc > 1:714513/1‑69 (MQ=255)
caTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGcc > 1:2711124/1‑69 (MQ=255)
caTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGcc > 1:1589771/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACttt > 1:2141138/1‑60 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTggg > 1:515424/1‑63 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTgg > 1:1052157/1‑62 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1574396/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:946309/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:929547/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:851254/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:786459/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:11442/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1547347/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:3058103/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2566891/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1610349/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2454573/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2406829/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1710278/1‑69 (MQ=255)
aTTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2096886/1‑69 (MQ=255)
aTTTCGAAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:7940/1‑69 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:1554541/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:3074807/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:2147246/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:2297241/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:1766372/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:2898425/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:1586066/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:2220079/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:2013780/68‑1 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1679638/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1285066/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1133073/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1063222/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1319310/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1059273/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:801084/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:3211537/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2998619/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2276592/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:2532687/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGACTTTGGGTTGCCg > 1:1603584/1‑64 (MQ=255)
gCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATCTCCGTGGCTTTGGGTTGCCGGTgg < 1:115823/68‑1 (MQ=255)
cAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTgg < 1:2632356/67‑1 (MQ=255)
ttAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTc > 1:199279/1‑69 (MQ=255)
aTGGGCTGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTcgcg > 1:438881/1‑69 (MQ=255)
aTGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTcgcg > 1:750983/1‑69 (MQ=255)
gggCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTcgcg < 1:860059/67‑1 (MQ=255)
gggCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTcgcg < 1:2555704/67‑1 (MQ=255)
ggCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTCGCGacc > 1:2508364/1‑69 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:752663/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:250349/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:214430/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:2553893/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:2688500/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:2185478/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:1068665/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:559003/38‑1 (MQ=255)
ccGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:294089/38‑1 (MQ=255)
cGTGACTTTGGGTTGCCGGTGGAATGGAGGCGTcccc < 1:3143207/37‑1 (MQ=255)
|
GGGCGGCAGCATTTCGCAAAGGTGATCAGCACGCCATCGGCACCTTTAATGGGCAGATGTCCGTGGCTTTGGGTTGCCGGTGGAATGGAGGCGTCCCCATGTTGCAGATTTTTCGCGACC > minE/2517348‑2517467
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
