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 |
2,284,647 |
G→A |
75.2% |
G297G (GGC→GGT) |
argH ← |
argininosuccinate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,284,647 | 0 | G | A | 75.2%
| 41.9
/ 11.2
| 41 | G297G (GGC→GGT) | argH | argininosuccinate lyase |
| Reads supporting (aligned to +/- strand): ref base G (5/5); new base A (10/20); total (15/26) |
| Fisher's exact test for biased strand distribution p-value = 4.57e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.44e-01 |
CCAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAATG > minE/2284592‑2284705
|
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:133492/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:864109/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:819768/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:741048/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:671972/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:352224/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:3435862/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:294058/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2840171/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2836367/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2786704/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2709935/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:241088/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2320236/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2317912/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2188905/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:1339834/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:1748230/66‑1 (MQ=255)
ccAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:2097670/66‑1 (MQ=255)
aGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAgcgc < 1:399636/68‑1 (MQ=255)
aGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAgcgc < 1:2733293/68‑1 (MQ=255)
gTCATCATCATGCCGGTTAACGCCCCCTGCACCCGACCGCATTTAc < 1:1868983/46‑1 (MQ=255)
tcatcatcaTGCCTGTTAACGCCCCCTGCACCCGCCCGCTTTTAc < 1:360295/45‑1 (MQ=255)
tAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCgg > 1:2921990/1‑69 (MQ=255)
tAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCgg > 1:1402763/1‑69 (MQ=255)
tAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCgg > 1:2582176/1‑69 (MQ=255)
aaCGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTttc < 1:2146453/60‑1 (MQ=255)
aaCGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTttc < 1:3196183/60‑1 (MQ=255)
aaCGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTttc < 1:22018/60‑1 (MQ=255)
aaCGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGc > 1:2124667/1‑69 (MQ=255)
aaCGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGc > 1:1714763/1‑69 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:962346/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:1190006/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:1603023/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:2269577/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:531246/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:1619164/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:3385100/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:3108803/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:3077233/1‑68 (MQ=255)
cTGCACCCGACCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAatg > 1:2168430/1‑68 (MQ=255)
|
CCAGCGGCAAACCTTTCAGCGTCATCATCATGCCGGTTAACGCCCCCTGCACCCGGCCGCATTTACCGCGAATCAGCTCCAGCGCATCCGGGTTTTTCTTCTGCGGCATTAATG > minE/2284592‑2284705
|
| 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
