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 |
1,176,179 |
T→C |
40.6% |
E63E (GAA→GAG) |
ydjA ← |
predicted oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,176,179 | 0 | T | C | 40.6%
| 20.6
/ 40.4
| 59 | E63E (GAA→GAG) | ydjA | predicted oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (16/19); new base C (14/10); total (30/29) |
| Fisher's exact test for biased strand distribution p-value = 4.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGCGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTGCATG > minE/1176111‑1176245
|
gcgcGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:3155989/69‑1 (MQ=255)
gcgcGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:2734330/69‑1 (MQ=255)
gcgcGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:650252/69‑1 (MQ=255)
gcgcGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:1836077/69‑1 (MQ=255)
gcgcGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:657314/69‑1 (MQ=255)
gcgcGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:723813/69‑1 (MQ=255)
cgcgGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGt < 1:841112/68‑1 (MQ=255)
gAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAg < 1:269713/69‑1 (MQ=255)
aTTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAg < 1:365209/60‑1 (MQ=255)
aCGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGaa > 1:2852747/1‑69 (MQ=255)
aCGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGaa > 1:1387626/1‑69 (MQ=255)
aCGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGa > 1:1754343/1‑68 (MQ=255)
cTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCt < 1:2555223/69‑1 (MQ=255)
cTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCt < 1:1946521/69‑1 (MQ=255)
gTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAg < 1:3075430/48‑1 (MQ=255)
tCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTcgc < 1:959702/67‑1 (MQ=255)
tgATTGCTTTGTTATCACTACCGGCAGCAAT‑‑CCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:1844612/67‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:911365/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:1020997/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:3210936/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:2452670/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:1347373/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:1426500/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:64313/69‑1 (MQ=255)
gATTGCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:2126429/69‑1 (MQ=255)
attgCTTTGTTATCACTACCGGCAGCAATCGCCCCCTGCTCCAGTACAGCGCTGAAACGCTCGCGccc < 1:1429487/65‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACg < 1:1431903/57‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACg < 1:19605/57‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACg < 1:1949125/57‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACg < 1:1604937/57‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACg < 1:772449/57‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGcccttc > 1:2637417/1‑69 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGcccttc < 1:2635034/69‑1 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGcccttc > 1:279822/1‑69 (MQ=255)
aGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGcccttc < 1:2922418/69‑1 (MQ=255)
caCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATc > 1:3394549/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:170304/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:397380/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:2483942/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:47138/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:557378/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:2219429/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:1499862/1‑68 (MQ=255)
aCTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATca > 1:1630988/1‑68 (MQ=255)
cGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACgg > 1:63946/1‑69 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAACCGCTCGCGcccttcccc > 1:127799/1‑43 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:2228874/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:1360762/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:136660/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:809910/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:1698093/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:2007523/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:2372947/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:2573458/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:2601045/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:3256613/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:3044568/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAGAAATGCCACGGt > 1:3055327/1‑68 (MQ=255)
cccccTGCTCCAGTACAGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCA‑AAAGAAATGCCACGGTTg > 1:1984937/1‑69 (MQ=255)
ccccTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTg < 1:3103224/69‑1 (MQ=255)
ccccTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTg < 1:2610976/69‑1 (MQ=255)
ccccTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTg < 1:1688072/69‑1 (MQ=255)
ccccTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTg < 1:165196/69‑1 (MQ=255)
ccccTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTg < 1:3209356/69‑1 (MQ=255)
cccTGTTCCAGTACGGCGCTGAAACGCTCGCGGCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTg < 1:1696742/68‑1 (MQ=255)
tGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTGCATg > 1:2465879/1‑69 (MQ=255)
|
GCGCGGAACGGCGCATTACGGGCTTTGTCGATAGCTTTGTCATCACTACCGGCAGCAATCGCCCCCTGTTCCAGTACGGCGCTGAAACGCTCGCGCCCTTCCCCTTCAATCACAAAAAAATGCCACGGTTGCATG > minE/1176111‑1176245
|
| 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
