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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,014,764 |
A→T |
36.1% |
S435S (TCT→TCA) |
fumA ← |
aerobic Class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,014,764 | 0 | A | T | 36.1%
| 30.3
/ 34.8
| 36 | S435S (TCT→TCA) | fumA | aerobic Class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base A (10/13); new base T (10/3); total (20/16) |
| Fisher's exact test for biased strand distribution p-value = 8.27e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.54e-01 |
ATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTAC > minE/1014696‑1014833
|
aTACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAagag > 1:5288592/1‑70 (MQ=255)
ctgccgccgTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAAc > 1:1768185/4‑70 (MQ=255)
tCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCg > 1:3303521/1‑70 (MQ=255)
ccgccgTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAAcctg < 1:2496049/70‑3 (MQ=255)
ccGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCAGTCCGGCGGTCGTTGGGCCAAGAGAACCg > 1:532879/1‑69 (MQ=255)
cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga > 1:73698/1‑58 (MQ=255)
cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga > 1:3284340/1‑58 (MQ=255)
cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga > 1:3919429/1‑58 (MQ=255)
cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga > 1:2758279/1‑58 (MQ=255)
cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga > 1:5226654/1‑58 (MQ=255)
ttGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAAcctg < 1:2145841/59‑3 (MQ=255)
tGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTc > 1:1543561/1‑71 (MQ=255)
tGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAgtga < 1:5144256/53‑1 (MQ=255)
tGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAACCTGATGGATAAccgg > 1:3406880/1‑68 (MQ=255)
gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTcc > 1:2276558/1‑71 (MQ=255)
agATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAACCTGATGGATAAccg > 1:1166034/2‑62 (MQ=255)
agATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAACCTGATGGATAAcc > 1:4609802/2‑62 (MQ=255)
gATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga > 1:5664825/1‑44 (MQ=255)
gATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGt < 1:2935683/70‑1 (MQ=255)
tCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGttt > 1:116620/1‑70 (MQ=255)
aCATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGc < 1:2207995/71‑1 (MQ=255)
aTAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCg > 1:1045288/1‑71 (MQ=255)
aaGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGa > 1:3023545/1‑71 (MQ=255)
gAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCAt > 1:429418/1‑46 (MQ=255)
atccatccGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGAccc > 1:2789702/1‑70 (MQ=255)
tccgtccgGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGttt < 1:3929613/54‑1 (MQ=255)
cgtcccGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCgtagta < 1:3608595/71‑1 (MQ=255)
ctgcggTGGTTGGGCCAAGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCgtag > 1:2669235/3‑65 (MQ=255)
tgcggTGGTTGGGCCAAGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCgtag > 1:3835326/2‑64 (MQ=255)
ggcggTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCg < 1:1963437/71‑1 (MQ=255)
cggTGGTTGGGCCAAGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCggg > 1:3979551/1‑70 (MQ=255)
ggTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGgat < 1:2927941/71‑1 (MQ=255)
gTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGgatg < 1:1281739/71‑1 (MQ=255)
gggCCAAGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCttt > 1:2622623/1‑71 (MQ=255)
gggCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCtt > 1:82283/1‑70 (MQ=255)
ggCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCttt < 1:3307703/70‑1 (MQ=255)
ggCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCttt < 1:549856/70‑1 (MQ=255)
ccAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTaaa < 1:830660/55‑1 (MQ=255)
ccAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTaaa < 1:1415740/55‑1 (MQ=255)
cAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATg < 1:5629680/71‑1 (MQ=255)
aaGTGAACCTGATGGATAACCGGCAGGTGTTTTCGCCGGACCcgc < 1:1037267/45‑1 (MQ=255)
aaGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATg > 1:2722137/1‑70 (MQ=255)
aaGTGAACCTGATGGATAACCGGCAGGGGTTTTCGCCGGACCCGCGTAGTAGATCGGGTGATCTTTGATg > 1:2967144/1‑70 (MQ=255)
aaGAGAACGGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATc < 1:961661/63‑1 (MQ=255)
gagaACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGga > 1:4586304/1‑56 (MQ=255)
gagaACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTAc > 1:47173/1‑71 (MQ=255)
agaACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCttt < 1:770335/63‑1 (MQ=255)
|
ATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCCGGCGTTTTGGCCGGACCCGCGTAGTAAATCGGATGATCTTTGATGTAC > minE/1014696‑1014833
|
| 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
