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 |
1,649,829 |
T→C |
60.9% |
T350T (ACT→ACC) |
yfgC → |
predicted peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,649,829 | 0 | T | C | 60.9%
| 36.7
/ 47.4
| 74 | T350T (ACT→ACC) | yfgC | predicted peptidase |
| Reads supporting (aligned to +/- strand): ref base T (8/21); new base C (22/23); total (30/44) |
| Fisher's exact test for biased strand distribution p-value = 9.10e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.57e-01 |
CGTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGAAAAATGCCCGC > minE/1649764‑1649889
|
cgTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGat < 1:172224/69‑1 (MQ=255)
cgTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGat < 1:579791/69‑1 (MQ=255)
cgTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGat < 1:3353662/69‑1 (MQ=255)
cgTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGat < 1:2351897/69‑1 (MQ=255)
cgTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGat < 1:2925171/69‑1 (MQ=255)
cgTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGat < 1:1221843/69‑1 (MQ=255)
aCGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGa < 1:543884/68‑1 (MQ=255)
aCGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGa < 1:1490352/68‑1 (MQ=255)
aCGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGa < 1:2903057/68‑1 (MQ=255)
aCGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGa < 1:2918175/68‑1 (MQ=255)
aCGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGa < 1:3076210/68‑1 (MQ=255)
aCGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGa < 1:103592/68‑1 (MQ=255)
gCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCt < 1:3370458/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATGtt < 1:2677361/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2521563/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2256132/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:688591/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2049237/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2787793/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2851481/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:3016365/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:3030368/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:3071856/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:344271/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1231881/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2007325/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1724182/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1001021/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1048139/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1998871/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1806631/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1057202/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1839789/69‑1 (MQ=255)
cTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:113040/69‑1 (MQ=255)
tGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:1844474/68‑1 (MQ=255)
tGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACCGATATCGATCtt < 1:2416913/68‑1 (MQ=255)
gAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAg < 1:1174593/69‑1 (MQ=255)
gAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAg < 1:1149014/69‑1 (MQ=255)
aCCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGc > 1:3350505/1‑69 (MQ=255)
ccTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCg > 1:3371808/1‑69 (MQ=255)
gCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAg < 1:1288796/57‑1 (MQ=255)
gTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGa < 1:3347191/68‑1 (MQ=255)
gTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGa > 1:2027865/1‑68 (MQ=255)
gTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGa < 1:1462240/68‑1 (MQ=255)
gTATCTCGATCTGGCTACTCATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGa < 1:958967/68‑1 (MQ=255)
tcGATCTGGCTACTGATATCGATCTTGGGCAAAACaa < 1:2637241/37‑1 (MQ=255)
tcGATCTGGCTACTGATATCGATCTTGGGCAAAACaa < 1:102571/37‑1 (MQ=255)
tcGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGc > 1:899078/1‑49 (MQ=255)
tcGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGAAAAATg > 1:2991605/1‑69 (MQ=255)
tcGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGAAAAATg > 1:2024603/1‑69 (MQ=255)
tcGATCTGGCTACTAATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGAAAAATg > 1:2072365/1‑69 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAAc > 1:2445978/1‑35 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:517402/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:861273/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:624991/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:499741/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:654503/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:993523/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:711815/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:698907/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:3415791/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2970385/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2760488/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2583173/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2527501/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2326029/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2160193/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2016751/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:2005676/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:1785171/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:1672487/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:1373410/1‑36 (MQ=255)
tcGATCTGGCTACCGATATCGATCTTGGGCAAAACa > 1:1026862/1‑36 (MQ=255)
cTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGAAAAATGCCcgc > 1:3329610/1‑69 (MQ=255)
|
CGTAAAACGCTGCAACCGTTACTGGCGGCAGAACCTGGCAACGCATGGTATCTCGATCTGGCTACTGATATCGATCTTGGGCAAAACAAAGCCAATGAGGCGATCAATCGTCTGAAAAATGCCCGC > minE/1649764‑1649889
|
| 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
