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 |
1,882,687 |
T→C |
31.6% |
V149V (GTA→GTG) |
relA ← |
(p)ppGpp synthetase I/GTP pyrophosphokinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,882,687 | 0 | T | C | 31.6%
| 47.9
/ 28.7
| 60 | V149V (GTA→GTG) | relA | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| Reads supporting (aligned to +/- strand): ref base T (22/19); new base C (3/16); total (25/35) |
| Fisher's exact test for biased strand distribution p-value = 1.02e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCGGAGGA > minE/1882624‑1882752
|
ttCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCa < 1:1037158/69‑1 (MQ=255)
ttCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCa < 1:1707587/69‑1 (MQ=255)
ttCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCa < 1:467521/69‑1 (MQ=255)
ccGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAat > 1:2856987/1‑69 (MQ=255)
ccGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAat > 1:1466667/1‑69 (MQ=255)
ccGGCGCATCTTTTACTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAat > 1:1454363/1‑69 (MQ=255)
cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc > 1:2878482/1‑67 (MQ=255)
cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc > 1:1987240/1‑67 (MQ=255)
cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc > 1:2630309/1‑67 (MQ=255)
cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc > 1:1983126/1‑67 (MQ=255)
cTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGAc > 1:2200071/1‑67 (MQ=255)
ttttACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCAt > 1:1287920/1‑69 (MQ=255)
ttttACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCAt > 1:177736/1‑69 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2132390/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:3359949/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2178268/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2196941/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2207241/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2315389/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:704763/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:1274307/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:3090946/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:3102358/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2022466/65‑1 (MQ=255)
aCTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:1521358/65‑1 (MQ=255)
aCTTCGCGCACGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:3022766/65‑1 (MQ=255)
aCTTCGCCCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:2078308/65‑1 (MQ=255)
cTTCGCGCAGGTGAGCAATACGCTCCGCCAGTTTGATGACCACGCAGCGAAAATCATCGACCAt < 1:3357073/64‑1 (MQ=255)
gcAGGTGAGCAATACGCTCCGCCTGTTTGATGACCACGCACCGAAAATCATCGACCAt < 1:2365965/58‑1 (MQ=255)
gAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCgg > 1:539210/1‑68 (MQ=255)
gAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCgg > 1:459008/1‑68 (MQ=255)
gAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCgg > 1:1734711/1‑68 (MQ=255)
gAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCgg > 1:2502835/1‑68 (MQ=255)
tACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGt > 1:2761929/1‑69 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGaa > 1:1580214/1‑64 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGtt > 1:1523546/1‑68 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa > 1:328165/1‑69 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa < 1:3109962/69‑1 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa > 1:3327121/1‑69 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa < 1:623258/69‑1 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa > 1:867540/1‑69 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa < 1:882634/69‑1 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa < 1:283680/69‑1 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa > 1:1682551/1‑69 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa < 1:1980739/69‑1 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa > 1:1977846/1‑69 (MQ=255)
cGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTa > 1:2468021/1‑69 (MQ=255)
gaCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCggaggt < 1:2113116/69‑2 (MQ=255)
gaCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCggagga < 1:1427257/69‑1 (MQ=255)
gaCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCggagga < 1:2399198/69‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:2395539/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:1629241/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:35635/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:1784200/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:135080/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:3238588/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:2791272/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATc < 1:2109558/53‑1 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCggagga > 1:316913/1‑68 (MQ=255)
aCTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCggagga > 1:1283263/1‑68 (MQ=255)
|
TTCATCTTCCGGCGCATCTTTTACTTCGCGCAGATGAGCAATACGCTCCGCCAGTTTGATGACTACGCAGCGAAAATCATCGACCATCGCCAATAACATCCGGCGAACGTTATCGACCTGTTCGGAGGA > minE/1882624‑1882752
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
