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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
608,072 |
G→T |
16.0% |
Q728K (CAG→AAG) ‡ |
pflB ← |
pyruvate formate lyase I |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 608,072 | 0 | G | T | 16.0%
| 163.2
/ 12.1
| 56 | Q728K (CAG→AAG) ‡ | pflB | pyruvate formate lyase I |
| Reads supporting (aligned to +/- strand): ref base G (27/20); new base T (3/6); total (30/26) |
| Fisher's exact test for biased strand distribution p-value = 2.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.82e-01 |
CCTGCTGCTGTTCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAGGTGC > minE/608006‑608142
|
ccTGCTGCTGTTCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGa > 1:145123/1‑71 (MQ=255)
ctgctgctgTTCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGa < 1:910165/70‑1 (MQ=255)
tgctgTTCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATAttt > 1:3792193/1‑71 (MQ=255)
tgctgTTCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATAttt > 1:1300684/1‑71 (MQ=255)
ttCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTcc < 1:1404730/70‑1 (MQ=255)
ttCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTcc < 1:2531698/70‑1 (MQ=255)
ttCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTcc < 1:2198588/70‑1 (MQ=255)
tAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGttt > 1:941510/1‑71 (MQ=255)
tCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTcc < 1:2401492/62‑1 (MQ=255)
aGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCAt > 1:1828542/1‑71 (MQ=255)
cGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTg < 1:2570363/45‑1 (MQ=255)
gatGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTACCGGGtttt > 1:1958951/3‑62 (MQ=255)
ttGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCg > 1:2265872/1‑43 (MQ=255)
gAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATAttttt > 1:1997915/1‑50 (MQ=255)
gAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTc > 1:2861031/1‑69 (MQ=255)
gAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCg < 1:2574956/70‑1 (MQ=255)
aaaCGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCCTCGag < 1:589931/71‑1 (MQ=255)
aaCGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGat < 1:1339895/42‑1 (MQ=255)
aaCGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCg > 1:1936877/1‑68 (MQ=255)
aCGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGag > 1:566372/1‑69 (MQ=255)
aCGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGag > 1:529629/1‑69 (MQ=255)
gTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGagca > 1:3640/1‑69 (MQ=255)
aCTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCAt > 1:3378394/1‑71 (MQ=255)
cggCGTAGCCAGAGACACGGATTGTCAGGTTAGGATATTTTTCCGGGTGCTCGATGGCATCCAGCAGCAtt < 1:3645971/69‑1 (MQ=12)
cggCGTAGCCAGAGACACGGATTGTCAGGTTAGGATATTTTTCCGGGTGCTCGATGGCATCCAGCAGCAtt < 1:1265563/69‑1 (MQ=12)
gCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCAttt > 1:2362056/1‑70 (MQ=255)
cGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCa > 1:2963865/1‑71 (MQ=255)
gCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGt < 1:3744660/71‑1 (MQ=255)
gCCAGAGACACGGATTGTCAGGTTAGGATATTTTTCCgg > 1:931519/1‑39 (MQ=9)
gCCAGAGACACGGATTGTCAGGTTAGGATATTTTTCCgg > 1:75985/1‑39 (MQ=9)
gCCAGAGACACGGATTGTCAGGTTAGGATATTTTTCCGGGtgc > 1:1021577/1‑41 (MQ=9)
cAGAGACACGGATTGTCAGGTTAGGATATTTTTCCGGGTGCTCGATGGCATCCAGCAGCATTTCCCga < 1:2729242/68‑2 (MQ=9)
agagACACGGATTGTCAGGTTAGGATATTTTTCCGGGTGCTCGATGGCATCCAGCAGCATTTCCCg < 1:263141/66‑1 (MQ=9)
aGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGtt < 1:871208/39‑1 (MQ=255)
aGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTtca > 1:396873/1‑71 (MQ=255)
aGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTtca < 1:385533/71‑1 (MQ=255)
taTACACGGATGGTCAGCTGCGGATATTTTTCCGGGttt > 1:454934/2‑39 (MQ=255)
gagacacGGATTGTCAGGTTAGGATATTTTTCCGGGTGCTCGATGGCATCCAGCAGCATTTCCCGATtcat < 1:803100/68‑1 (MQ=9)
gATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCAttt < 1:303918/61‑1 (MQ=255)
aTACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTtcat > 1:3380607/1‑70 (MQ=255)
acacGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCAc > 1:1149639/1‑71 (MQ=255)
cacGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCAc < 1:251882/70‑1 (MQ=255)
acGGATGGTCAGCTGCGGAAATTTTTCCGGGTTTTCCATCGCGTCGagcagc > 1:25087/1‑52 (MQ=255)
ggATTGTCAGGTTAGGATATTTTTCCGGGTGCTCGATGGCATCCAGCAGCATTTCCCGATTCATTACGttg < 1:1812077/71‑2 (MQ=255)
ggATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGtt > 1:2612834/1‑70 (MQ=255)
gTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCAttt < 1:731714/49‑1 (MQ=255)
tCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCAc < 1:160098/51‑1 (MQ=255)
tCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTc < 1:928150/71‑1 (MQ=255)
cAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGtt > 1:254837/1‑69 (MQ=255)
aGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAg < 1:3241491/71‑1 (MQ=255)
aGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAg > 1:3155460/1‑71 (MQ=255)
aGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAg > 1:1010417/1‑71 (MQ=255)
gCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTtcatc > 1:2916952/1‑56 (MQ=255)
gCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCa < 1:1912623/69‑1 (MQ=255)
cTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAGGt < 1:2538351/71‑1 (MQ=255)
cTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAGGt > 1:40621/1‑71 (MQ=255)
cTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAGGt < 1:3583132/71‑1 (MQ=255)
gCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAGGTGc > 1:3690568/1‑71 (MQ=255)
|
CCTGCTGCTGTTCTTTAGTCAGCGAGTTGAAACGTACTGCGTAGCCAGATACACGGATGGTCAGCTGCGGATATTTTTCCGGGTTTTCCATCGCGTCGAGCAGCATTTCACGGTTCATCACGTTAACGTTCAGGTGC > minE/608006‑608142
|
| 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
