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 |
2,640,112 |
A→C |
24.4% |
T45T (ACT→ACG) |
yhhA ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,640,112 | 0 | A | C | 24.4%
| 57.7
/ 21.0
| 45 | T45T (ACT→ACG) | yhhA | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (5/29); new base C (2/9); total (7/38) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01 |
GCTGTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTG > minE/2640048‑2640175
|
tctgTTGCTACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTc < 1:429275/67‑1 (MQ=255)
gctgTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTc < 1:2236033/68‑1 (MQ=255)
gctgTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTc < 1:2121085/68‑1 (MQ=255)
gctgTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTc < 1:522189/68‑1 (MQ=255)
gTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGc < 1:2403116/68‑1 (MQ=255)
gTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCa < 1:149394/69‑1 (MQ=255)
gCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCt > 1:1365176/1‑69 (MQ=255)
gCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCt > 1:157426/1‑69 (MQ=255)
tGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTggg < 1:1538405/68‑1 (MQ=255)
tGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTggg < 1:2566505/68‑1 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:1244942/66‑2 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:1663121/66‑2 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:1929639/66‑2 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:3392958/66‑2 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:2613744/66‑2 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:142298/66‑2 (MQ=255)
ggttCAGCATCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTgggg < 1:943007/66‑2 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGTCTGGGTa < 1:2587048/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:2845343/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:3218226/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:3135859/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:304885/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:3398275/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:1957502/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:554418/69‑1 (MQ=255)
gATTCAGCATCCCTTTTTGCTGGATTTGCTGAGGCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTa < 1:526671/69‑1 (MQ=255)
cAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCt > 1:611344/1‑68 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:391274/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:421790/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:3191934/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:577602/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:3112868/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:2934609/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:1569732/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:2836901/68‑1 (MQ=255)
gCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:2209446/68‑1 (MQ=255)
cATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGa < 1:996541/67‑1 (MQ=255)
aTCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATat > 1:469069/1‑68 (MQ=255)
aTCCCTTTTTGCTGGATTTGCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATat > 1:3111371/1‑68 (MQ=255)
ccTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATAcccc > 1:1925114/1‑69 (MQ=255)
ccTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATAccc > 1:1873471/1‑68 (MQ=255)
tGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGtt < 1:3236871/68‑1 (MQ=255)
tGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGtt < 1:2673144/68‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:1784800/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:3016842/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:966463/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:1376178/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:901125/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:774175/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:632429/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:628501/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:1567492/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:2852326/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:1957197/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:2078355/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:351757/69‑1 (MQ=255)
tgctgcGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:221533/69‑1 (MQ=255)
gCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:2982622/68‑1 (MQ=255)
gCTGCGTCTGCATTTGAGTTTGCATCCGCTGCTGGCTGGGGATCTGATATCCCGGCTGGTTAGGgttg < 1:356663/68‑1 (MQ=255)
|
GCTGTTGCAACTGAGTTTGCGTTTTCAGTTGCTGATTCAGCATCCCTTTTTGCTGGATTTGCTGAGTCTGCATCTGGGTTTGCATCCGCTGCTGGCTGGGTATCTGATACCCCGGCTGGTTAGGGTTG > minE/2640048‑2640175
|
| 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
