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 |
1,981,463 |
G→A |
33.2% |
D204D (GAC→GAT) |
yggR ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,981,463 | 0 | G | A | 33.2%
| 58.4
/ 35.8
| 72 | D204D (GAC→GAT) | yggR | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base G (36/12); new base A (16/8); total (52/20) |
| Fisher's exact test for biased strand distribution p-value = 5.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGCCCGCAATCCC > minE/1981400‑1981523
|
tAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTc > 1:29522/1‑66 (MQ=255)
tAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCa > 1:990906/1‑67 (MQ=255)
tAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCa > 1:3265013/1‑67 (MQ=255)
tAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCa > 1:401940/1‑67 (MQ=255)
tAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCa > 1:1621772/1‑67 (MQ=255)
tAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCa > 1:684219/1‑67 (MQ=255)
tAATGTCGCCAGCACCAGATGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACg < 1:1868044/69‑1 (MQ=255)
tAATGTCGCCAGCACCAGATGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACg < 1:2691919/69‑1 (MQ=255)
tAATGTCGCCAGCACCAGATGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACg < 1:1406740/69‑1 (MQ=255)
tAATGTCGCCAGCACCAGATGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACg < 1:1441992/69‑1 (MQ=255)
tAATGTCGCCAGCACCAGATGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACg < 1:826551/69‑1 (MQ=255)
ttGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCCCGCAGct > 1:659618/1‑69 (MQ=255)
ttGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGct > 1:1123070/1‑69 (MQ=255)
gCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTc > 1:3248360/1‑59 (MQ=255)
aTGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAAt < 1:645192/69‑1 (MQ=255)
aTGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAAt < 1:2643342/69‑1 (MQ=255)
aTGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACGCAGCTCTCCGAGCAAAAt < 1:1272936/69‑1 (MQ=255)
aTGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACGCAGCTCTCCGAGCAAAAt < 1:2625255/69‑1 (MQ=255)
tGCCCGGTTTCTGCCGCCGTCAGCGCCAGACGGATTGTCTCGCTATCACGCAGCTCTCCGAGCAAAAt < 1:2209704/68‑1 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATGAgg < 1:182052/69‑1 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg < 1:2170394/69‑1 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:3070344/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:3399/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg < 1:2269536/69‑1 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg < 1:2570556/69‑1 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:2382490/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:1106750/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:3270675/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:2793704/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:3399130/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:984450/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:1543771/1‑69 (MQ=255)
ttCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:1243928/1‑69 (MQ=255)
ttCTGCAGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAgg > 1:437026/1‑69 (MQ=255)
gccgccGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCt > 1:1809824/1‑69 (MQ=255)
gccgccGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCt > 1:2941479/1‑69 (MQ=255)
gccgccGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCt > 1:2294390/1‑69 (MQ=255)
gccgccGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCt > 1:1931874/1‑69 (MQ=255)
gccgccGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCt > 1:1595043/1‑69 (MQ=255)
gccgccGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCt > 1:1357160/1‑69 (MQ=255)
aGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCTCATCAGGATCTTCCCGCAAt > 1:514446/1‑69 (MQ=255)
aGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAAt > 1:2868990/1‑69 (MQ=255)
aGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAAt > 1:1051974/1‑69 (MQ=255)
aGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAAt > 1:2759316/1‑69 (MQ=255)
aGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAAt > 1:1775873/1‑69 (MQ=255)
gCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCg > 1:2585119/1‑69 (MQ=255)
ccAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGc > 1:1926818/1‑38 (MQ=255)
ccAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCgg > 1:2907548/1‑69 (MQ=255)
ccAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCgg > 1:2469154/1‑69 (MQ=255)
aGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGcc < 1:2202103/69‑1 (MQ=255)
aGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGcc < 1:1801850/69‑1 (MQ=255)
aGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGcc < 1:592035/69‑1 (MQ=255)
aGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGcc < 1:587010/69‑1 (MQ=255)
aCGTATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:112277/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:861820/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1193117/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1005842/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:822124/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:27469/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:765038/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1216862/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1353824/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:543914/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1522493/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1563460/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1650254/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:1980802/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:3132444/1‑36 (MQ=255)
aCGGATTGTCTCGCTATCACGCAGCTCTCCGAGCaa > 1:2008572/1‑36 (MQ=255)
cGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAAt > 1:1386091/1‑38 (MQ=255)
gTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGCCCGCAATccc < 1:1810953/69‑1 (MQ=255)
gTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGCCCGCAATccc < 1:2488867/69‑1 (MQ=255)
|
TAATGTTGCCAGCACCAAATGCCCGGTTTCTGCCGCCGTCAGTGCCAGACGGATTGTCTCGCTGTCACGCAGCTCTCCGAGCAAAATCACATCAGGATCTTCCCGCAATGCGGCCCGCAATCCC > minE/1981400‑1981523
|
| 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
