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 |
511,700 |
C→A |
29.3% |
P581P (CCC→CCA) |
ybhJ → |
predicted hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 511,700 | 0 | C | A | 29.3%
| 95.8
/ 34.8
| 68 | P581P (CCC→CCA) | ybhJ | predicted hydratase |
| Reads supporting (aligned to +/- strand): ref base C (19/29); new base A (10/10); total (29/39) |
| Fisher's exact test for biased strand distribution p-value = 5.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GAAACCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCGGGGAATGT > minE/511635‑511762
|
gAAACCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGt > 1:1786213/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAggg > 1:3176068/1‑68 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAgg > 1:1107020/1‑68 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:44516/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:2297477/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:24264/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:2438641/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:1934504/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:2550664/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:2762203/1‑69 (MQ=255)
gAAACCTCTTCATATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGt > 1:2921522/1‑69 (MQ=255)
aCCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTa > 1:1179/1‑68 (MQ=255)
aCCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTa < 1:340364/68‑1 (MQ=255)
aCCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTa < 1:491834/68‑1 (MQ=255)
aCCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTa < 1:2224982/68‑1 (MQ=255)
aCCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTa < 1:2559533/68‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:2220091/69‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:2189004/69‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:209880/69‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:1184506/69‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:533397/69‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:1644619/69‑1 (MQ=255)
tcttctTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGtt < 1:386894/69‑1 (MQ=255)
cttATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGTTAg < 1:1677678/67‑1 (MQ=255)
cttATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGTTAg < 1:2797675/67‑1 (MQ=255)
cttATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGTTAg < 1:2108237/67‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:723923/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:3069254/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:1444596/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:2127690/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:2906559/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:2789935/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:155108/68‑1 (MQ=255)
aTTGGTCTGGCGGAGTTTACTCTGTCACGCCGCGATCCAGGTTATGTTGGCAGAAGTAAAGCGActgc < 1:1447213/68‑1 (MQ=255)
cTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCg < 1:29598/57‑1 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:1076560/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:1175288/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:2080624/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:546524/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:2869090/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:2569035/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:2749454/1‑45 (MQ=255)
tACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGc > 1:1828658/1‑45 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:2203150/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:1252590/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:1616532/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:1815443/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:2685142/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:183761/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:2530307/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:2155524/1‑69 (MQ=255)
gTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGc > 1:3408514/1‑69 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:3237569/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:411278/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:962960/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:2948825/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:2935992/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:2447715/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:2330311/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:225575/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:1759093/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:1674695/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:1411773/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:1100151/66‑1 (MQ=255)
cgcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:1095621/66‑1 (MQ=255)
gcgATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCgggg < 1:1886061/65‑1 (MQ=255)
cgATCCAGGTTATGTTGGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCGGGAAATGt < 1:141210/69‑1 (MQ=255)
gATCCAGGTTATGTTGGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCGGGAAATGt < 1:2568481/68‑1 (MQ=255)
|
GAAACCTCTTCTTATCGTTCAAATCCGATTGGTCTGGCGGAGTTTACCCTGTCTCGCCGCGATCCCGGTTATGTTAGCAGAAGTAAAGCGACTGCTGAGCTGGAAAATCAGCGTCTGGCGGGGAATGT > minE/511635‑511762
|
| 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
