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 |
2,636,862 |
C→T |
73.7% |
D195D (GAC→GAT) |
ugpA → |
glycerol‑3‑phosphate transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,636,862 | 0 | C | T | 73.7%
| 55.3
/ 18.5
| 53 | D195D (GAC→GAT) | ugpA | glycerol‑3‑phosphate transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (6/8); new base T (7/32); total (13/40) |
| Fisher's exact test for biased strand distribution p-value = 8.01e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.69e-01 |
ACTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTTTCTTC > minE/2636795‑2636928
|
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:1040494/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:855334/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:3353191/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:3306490/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:2797918/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:120778/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:2644620/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:2570204/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:137021/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:1377042/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:2434634/68‑1 (MQ=255)
aCTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:1387030/68‑1 (MQ=255)
cTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGACgg < 1:987735/69‑1 (MQ=255)
cTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGACgg < 1:2316602/69‑1 (MQ=255)
cttctATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGAc < 1:2124938/58‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:1031471/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:2667600/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:2663534/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:300629/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:3080323/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:3366540/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:2469017/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:1383570/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:483398/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:1387840/66‑1 (MQ=255)
ccGCGCTGCAATCCATCCCCCGTGCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:2004674/66‑1 (MQ=255)
cgcgCTGCAATCCATCCCCCGTTCGTTGATCGAAGCGGCAGCCATTGATGGGGCAGGGCCGATTc < 1:1071791/65‑1 (MQ=255)
cgcgCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:1770924/65‑1 (MQ=255)
cgcgCTGCAATCCATCCCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:2682205/65‑1 (MQ=255)
gCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGACTGTGCAGGGCCGATTCGCCGcttct < 1:1161939/68‑1 (MQ=255)
atccatccCCCGTTCGTTGATCGAAGCCGCAGCCATTGATGGGGCAGGGCAGATTc < 1:2918188/56‑1 (MQ=255)
cGAAGCCGCAGCCATTGATGGGGCAGGGCCGATTc < 1:202259/35‑1 (MQ=25)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:493147/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:545134/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:68693/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1118285/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:698173/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:2751717/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1552493/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1516548/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1966547/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:2103652/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:2327126/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1888823/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1262664/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:259481/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGCCGCtgc < 1:1238964/63‑3 (MQ=255)
aaGCCTCAGCAATGGATGGTGCAGGTCCATTCCAGAACTTCTTTAAGATTACGCTGACGCtgc < 1:4354/63‑3 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCTGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:3248129/1‑66 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCCGATTCGGCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:1920997/1‑66 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:258059/1‑66 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:3288815/1‑66 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:248320/1‑66 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:2470867/1‑66 (MQ=255)
aGCCGCAGCCATTGATGGGGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGctc > 1:2410805/1‑66 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttcttc > 1:2898814/1‑69 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttcttc > 1:842307/1‑69 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct > 1:97823/1‑67 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct < 1:847265/67‑1 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct < 1:1088811/67‑1 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct < 1:3425775/67‑1 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct > 1:3258402/1‑67 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct > 1:2492884/1‑67 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct > 1:2848740/1‑67 (MQ=255)
gACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct < 1:2733979/67‑1 (MQ=255)
aCGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTttct < 1:2693042/66‑1 (MQ=255)
|
ACTTCCTGTTCTTCTATGCCGCGCTGCAATCCATTCCCCGTTCGTTGATCGAAGCCGCAGCCATCGACGGTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGCTGCCGCTTATCGCCCCGGTGAGTTTCTTC > minE/2636795‑2636928
|
| 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
