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 |
2,246,530 |
T→C |
29.3% |
G81G (GGT→GGC) |
thiC → |
thiamin (pyrimidine moiety) biosynthesis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,246,530 | 0 | T | C | 29.3%
| 66.0
/ 29.2
| 68 | G81G (GGT→GGC) | thiC | thiamin (pyrimidine moiety) biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base T (43/5); new base C (8/12); total (51/17) |
| Fisher's exact test for biased strand distribution p-value = 5.15e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
AGCAAAGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATGCGC > minE/2246462‑2246597
|
aGCAAAGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGt > 1:447449/1‑69 (MQ=255)
aaGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCTGTCTACGACACCTCCGGCCCGTATGGTGATc < 1:1463555/69‑1 (MQ=255)
aaGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc < 1:1506843/69‑1 (MQ=255)
aGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc < 1:1668164/68‑1 (MQ=255)
aGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc < 1:3427070/68‑1 (MQ=255)
aGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc < 1:2594984/68‑1 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:2737740/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:3387573/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:3311238/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:3096188/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:2999168/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:1307383/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:1283786/1‑66 (MQ=255)
aaCAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATc > 1:2887821/1‑66 (MQ=255)
gCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTg > 1:1569090/1‑68 (MQ=255)
gCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTg > 1:2683070/1‑68 (MQ=255)
gCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTg > 1:2248704/1‑68 (MQ=255)
gCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTg > 1:3337803/1‑68 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:2627979/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:3140486/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:2141788/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:207332/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:3398720/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:1928998/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:171432/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:1330964/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:1291207/69‑1 (MQ=255)
aCGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:1079652/69‑1 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:1773763/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:1771395/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:232537/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:1535707/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:3079204/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:1510760/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:2671465/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTaa > 1:1211756/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:1177248/68‑1 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGTCCGTATGGCGATCCGCAGATCGCCATTa < 1:534856/68‑1 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCa > 1:2710793/1‑57 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTaa > 1:280636/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTaa > 1:2810329/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTaa > 1:1939589/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTaa > 1:298021/1‑69 (MQ=255)
cGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTaa > 1:837904/1‑69 (MQ=255)
gCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAggg > 1:1319477/1‑69 (MQ=255)
gCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAggg > 1:1391099/1‑69 (MQ=255)
gCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAggg > 1:1841543/1‑69 (MQ=255)
gCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAggg > 1:2448481/1‑69 (MQ=255)
gCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAggg > 1:2567655/1‑69 (MQ=255)
gCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAggg > 1:858596/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:3097816/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:3099152/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:262835/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:2982035/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:3349629/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:2690262/1‑69 (MQ=255)
tACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTa > 1:1633548/1‑69 (MQ=255)
aTGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCg > 1:2693108/1‑66 (MQ=255)
aTGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATg > 1:2080443/1‑69 (MQ=255)
aTGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATg > 1:492246/1‑69 (MQ=255)
aTGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATg > 1:488356/1‑69 (MQ=255)
tGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgc > 1:623070/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:2043356/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:671020/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:687174/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:3030886/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:2819381/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:998535/1‑69 (MQ=255)
gTGATCCGCAGATTGCCATTAACGTGCAGCAACGGCTGGCAAAACTACGCCAGCCGTGGATCGATgcgc > 1:255138/1‑69 (MQ=255)
|
AGCAAAGAACAGCCGCAGTACGAAGAAAACGAAGCGATTCCGGTCTACGACACCTCCGGCCCGTATGGTGATCCGCAGATTGCCATTAACGTGCAGCAAGGGCTGGCAAAACTACGCCAGCCGTGGATCGATGCGC > minE/2246462‑2246597
|
| 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
