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 |
1,840,037 |
A→G |
62.4% |
N311N (AAT→AAC) |
truD ← |
pseudoruidine synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,840,037 | 0 | A | G | 62.4%
| 38.5
/ 41.7
| 69 | N311N (AAT→AAC) | truD | pseudoruidine synthase |
| Reads supporting (aligned to +/- strand): ref base A (17/9); new base G (26/17); total (43/26) |
| Fisher's exact test for biased strand distribution p-value = 7.99e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.32e-01 |
CGCTGGTTGCAAAACTACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACTTTTTC > minE/1839973‑1840096
|
cGCTGGTTGCAAAACTACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTcc < 1:3076457/69‑1 (MQ=255)
cGCTGGTTGCAAAACTACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTcc < 1:2116341/69‑1 (MQ=255)
cGCTGGTTGCAAAACTACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTcc < 1:1526455/69‑1 (MQ=255)
cGCTGGTTGCAAAACTACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTcc < 1:1305815/69‑1 (MQ=255)
tACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCg < 1:504191/69‑1 (MQ=255)
cccGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGa > 1:2322898/1‑69 (MQ=255)
cccGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGa > 1:2849187/1‑69 (MQ=255)
ccgccgGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTcc < 1:1424409/51‑1 (MQ=255)
ggAAGCCAGAAACGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATAcagc > 1:1673415/1‑69 (MQ=255)
ggAAGCCAGAAACGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATAcagc > 1:2303606/1‑69 (MQ=255)
ggAAGCCAGAAACGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATAcagc > 1:837414/1‑69 (MQ=255)
ggAAGCCAGAAACGGATTTATACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATAcagc > 1:3416051/1‑69 (MQ=255)
aGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACagcagc > 1:870590/1‑69 (MQ=255)
aGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACagcagc > 1:724664/1‑69 (MQ=255)
aGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACagcagc > 1:2492122/1‑69 (MQ=255)
aGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACagcagc > 1:1449671/1‑69 (MQ=255)
aGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACagcagc > 1:2240396/1‑69 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:3281909/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:982223/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:51245/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:383403/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:274003/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:758732/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:473033/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:2124837/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:513315/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:1992392/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:1518235/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:1708510/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:1844810/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:773702/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:1942740/69‑1 (MQ=255)
aaaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:1849303/69‑1 (MQ=255)
aaCGGATTTCTACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGct < 1:751768/68‑1 (MQ=255)
gATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGa < 1:705144/49‑1 (MQ=255)
gATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGa < 1:701894/49‑1 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1609053/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1432895/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1487668/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:149131/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:3378469/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:3290754/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:3240253/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:708532/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:3120794/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:2971049/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:291077/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:2861734/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:781103/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:2782521/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:2774181/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1899152/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:2726092/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1046646/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1845844/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1847844/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGCTTAATTGTTGCGGATACAGCAGCAACGCTCTgcgc > 1:846787/4‑69 (MQ=255)
atttctACGGTGACGTCATCCCACCAGTTCCAGATTAATTGTTGCGGATACAGCAGCATCGCTCTgcgc > 1:1210871/4‑69 (MQ=255)
gTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCa > 1:262349/1‑69 (MQ=255)
tGACATCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCaa < 1:1188347/69‑1 (MQ=255)
gTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACttt > 1:246870/1‑69 (MQ=255)
gTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACttt > 1:2325150/1‑69 (MQ=255)
gTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACttt > 1:2004331/1‑69 (MQ=255)
gTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACttt > 1:1731926/1‑69 (MQ=255)
gTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACttt > 1:1594838/1‑69 (MQ=255)
aTCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACTTTTTc > 1:3165698/1‑69 (MQ=255)
aTCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACTTTTTc > 1:292998/1‑69 (MQ=255)
aTCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACTTTTTc > 1:1661597/1‑69 (MQ=255)
aTCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACTTTTTc > 1:1103444/1‑69 (MQ=255)
|
CGCTGGTTGCAAAACTACCCGCCGGAAGCCAGAAACGGATCTCTACGGTGACGTCATCCCACCAATTCCAGCTTAATTGTTGCGGATACAGCAGCATCGCTCTGCGCGCGGCTTCAACTTTTTC > minE/1839973‑1840096
|
| 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
