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 |
554,039 |
C→A |
46.1% |
S139S (TCG→TCT) |
ybiY ← |
predicted pyruvate formate lyase activating enzyme |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 554,039 | 0 | C | A | 46.1%
| 11.3
/ 37.6
| 39 | S139S (TCG→TCT) | ybiY | predicted pyruvate formate lyase activating enzyme |
| Reads supporting (aligned to +/- strand): ref base C (8/13); new base A (8/10); total (16/23) |
| Fisher's exact test for biased strand distribution p-value = 7.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.60e-01 |
CTCGTGGCTGGCTTGCAGTAGCGCCATCGCCATTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATG > minE/553979‑554102
|
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:915567/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:647061/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:390170/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:1625375/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:3314223/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:3118498/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:3078550/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:3054992/69‑1 (MQ=255)
ctCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:2895660/69‑1 (MQ=255)
tCGTGGCTGGCTTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGt < 1:1694716/68‑1 (MQ=255)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:2664145/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:499818/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:3410239/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:3384847/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:289767/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:2630402/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:2590993/1‑69 (MQ=25)
ggctTGCAGCAGCGCCGTCGCCATTTCCGGCTGCATAAACGGTTCACCGCCAGAAAGCGTTAAgccgcc > 1:1342487/1‑69 (MQ=25)
gcgcCATCGCCATTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGAt > 1:1336350/1‑69 (MQ=255)
gcgcCATCGCCATTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGAt > 1:541103/1‑69 (MQ=255)
gcgcCATCGCCATTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGAt > 1:1921113/1‑69 (MQ=255)
gcgcCATCGCCATTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGAt > 1:1978631/1‑69 (MQ=255)
gccatcgccatTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGAt > 1:2970276/1‑67 (MQ=255)
gccatcgccatTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATc > 1:3022680/1‑68 (MQ=255)
gccatcgccatTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATc > 1:1775444/1‑68 (MQ=255)
gggCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACgg < 1:683021/68‑1 (MQ=255)
gggCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACgg < 1:3240785/68‑1 (MQ=255)
gggCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACgg < 1:2729036/68‑1 (MQ=255)
gggCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACgg < 1:1664293/68‑1 (MQ=255)
ccaccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCAt > 1:1438154/1‑68 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2628291/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2386954/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2663002/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:1330183/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:1444967/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2823906/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2215333/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2239754/68‑1 (MQ=255)
caccCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATg < 1:2252242/68‑1 (MQ=255)
|
CTCGTGGCTGGCTTGCAGTAGCGCCATCGCCATTTCCGGCTGCATAAAGGGCTCACCACCCGAAAGCGTTAAACCGCCGCCGCTGCGATCGTAAAACGGTTTATCGCGCAGAACGGTCGTCATG > minE/553979‑554102
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
