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 |
1,259,181 |
G→C |
45.1% |
A581A (GCC→GCG) |
torZ ← |
trimethylamine N‑oxide reductase system III, catalytic subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,259,181 | 0 | G | C | 45.1%
| 10.4
/ 55.5
| 51 | A581A (GCC→GCG) | torZ | trimethylamine N‑oxide reductase system III, catalytic subunit |
| Reads supporting (aligned to +/- strand): ref base G (16/12); new base C (17/6); total (33/18) |
| Fisher's exact test for biased strand distribution p-value = 2.51e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGTATAG > minE/1259119‑1259247
|
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCAcc > 1:3215139/1‑68 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCAcc > 1:1287253/1‑68 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1155103/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1131814/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:3214302/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1965783/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1709657/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:378268/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:401612/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1658017/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:51956/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:649823/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1396320/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1217421/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1207930/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:871249/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:910305/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 1:1467260/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 1:16974/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 1:3404045/1‑69 (MQ=255)
tATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCg > 1:2287713/1‑68 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:738051/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:3105383/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:310206/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:3031293/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:2747374/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:2173266/69‑1 (MQ=255)
aTAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTc < 1:2164641/68‑1 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGc > 1:1699427/1‑35 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:1173992/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:2964709/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:843806/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:1284415/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:2076418/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:1429181/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:1588544/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGaaaa > 1:3384713/1‑46 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGc > 1:929903/1‑54 (MQ=255)
gTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATc > 1:1806507/1‑68 (MQ=255)
gTGACGCGTTGCGCACGGGCACATTTCTGAGCGGCATCATAGaaaa > 1:2814972/1‑46 (MQ=255)
gcagggCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:1869911/65‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:3431214/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:382670/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:1699392/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:3365176/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:628694/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:3064922/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:2661986/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:2857776/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:881042/68‑1 (MQ=255)
cACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGta < 1:2700716/68‑1 (MQ=255)
cGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGTATAg < 1:116296/69‑1 (MQ=255)
|
TCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTCATCTTTACCTTCGGTATAG > minE/1259119‑1259247
|
| 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
