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 |
2,444,536 |
G→A |
47.1% |
T200T (ACC→ACT) |
ilvD ← |
dihydroxyacid dehydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,444,536 | 0 | G | A | 47.1%
| 9.1
/ 73.6
| 87 | T200T (ACC→ACT) | ilvD | dihydroxyacid dehydratase |
| Reads supporting (aligned to +/- strand): ref base G (29/17); new base A (3/38); total (32/55) |
| Fisher's exact test for biased strand distribution p-value = 3.56e-08 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01 |
CGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGATCGCTC > minE/2444476‑2444596
|
cGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:793370/69‑1 (MQ=255)
cGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:2794870/69‑1 (MQ=255)
cGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:2655869/69‑1 (MQ=255)
cGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:2584047/69‑1 (MQ=255)
cGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:1640115/69‑1 (MQ=255)
cGAGCCGTTGCCCGGCTGCGACAGG‑CCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:514612/68‑1 (MQ=255)
gAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACAt < 1:1503449/68‑1 (MQ=255)
ccGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTATACATCCCg < 1:1617255/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:1166431/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:96716/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:768367/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:70717/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:3116070/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:2987508/69‑1 (MQ=255)
cGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:2267369/69‑1 (MQ=255)
gTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:2955690/68‑1 (MQ=255)
gTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCgg < 1:2034267/68‑1 (MQ=255)
gCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGc > 1:3280021/1‑69 (MQ=255)
gCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGc > 1:1934319/1‑69 (MQ=255)
gCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGc > 1:821362/1‑69 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTATCGGTAAACATCCCGGa > 1:2135675/1‑45 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGacac > 1:2471608/1‑67 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACAcg > 1:3371579/1‑68 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACAcg > 1:124405/1‑68 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACAcg > 1:3311570/1‑68 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACAcg > 1:316725/1‑68 (MQ=255)
cgcTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACAcg > 1:3299848/1‑68 (MQ=255)
cAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCaa > 1:1484182/1‑67 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGTCGGATCGTTCAAcc < 1:3067542/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:1543021/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:3389149/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:3254161/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:454886/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:537603/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:2875592/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:2810334/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:2547019/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:1763040/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:2267242/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:811390/69‑1 (MQ=255)
cAGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:2048398/69‑1 (MQ=255)
aGTTCATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:3030078/68‑1 (MQ=255)
tCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGAt > 1:3214262/1‑69 (MQ=255)
tCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGAt > 1:916476/1‑69 (MQ=255)
tCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGAt > 1:2831960/1‑69 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTc > 1:3094782/1‑60 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2412417/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:150640/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:1501089/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2062197/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2197915/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2953289/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2213707/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:492634/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:1286140/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:1284510/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2291706/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:583522/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:2697501/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCa > 1:1438589/1‑61 (MQ=255)
cATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGAAGGTCGGACACGCGGAACGTTCa > 1:3283842/1‑61 (MQ=255)
cATTGAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:159038/64‑1 (MQ=255)
tGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGATCGct > 1:3041085/1‑69 (MQ=255)
tGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGATCGct > 1:3420366/1‑69 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATGGTTCAACCTGAGCGctc < 1:681970/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1143863/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1327774/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1727130/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:855580/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:850686/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1986085/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:2010370/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1180875/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:2151698/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:732413/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1486262/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:662026/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:577737/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:2906666/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:2944867/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:486574/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:2952492/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:3418929/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:3408525/69‑1 (MQ=255)
gAGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:1331613/69‑1 (MQ=255)
aGTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTTGGCAGGCGGATCGTTCAACCTGAGCGctc < 1:2884720/68‑1 (MQ=255)
gTTAGCAGTAAACATCCCGGAGCAGGAACCGCAGGTTGGGCAGGCGGATCGTTCAAcc < 1:1382845/58‑1 (MQ=255)
|
CGAGCCGTTGCCCGGCTGCGACAGGCCCAGCGCTTCGGTCAGGCAGTTCATTGAGTTAGCGGTAAACATCCCGGAGCAGGAACCGCAGGTCGGACACGCGGAACGTTCAACCTGATCGCTC > minE/2444476‑2444596
|
| 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
