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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,588,010 |
T→G |
100% |
D64A (GAC→GCC) |
ydeP ← |
predicted oxidoreductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,588,010 | 0 | T | G | 93.7%
| 154.3
/ ‑1.4
| 47 | D64A (GAC→GCC) | ydeP | predicted oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base T (0/3); new base G (24/20); total (24/23) |
| Fisher's exact test for biased strand distribution p-value = 1.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGAAAGAGGCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGTCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGACAGTCAAAGCCCTCTGGCTTAT > W3110S.gb/1587942‑1588076
|
agaaagaGGCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGTCg < 1:1269654/71‑1 (MQ=255)
agaaagaGGCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCg < 1:2554822/71‑1 (MQ=255)
aagaGGCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAAt < 1:1363185/71‑1 (MQ=255)
aagaGGCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAAt < 1:3717179/71‑1 (MQ=255)
gCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGc < 1:559165/71‑1 (MQ=255)
gTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCAc < 1:1909709/71‑1 (MQ=255)
gTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCAc < 1:2481610/71‑1 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCAc < 1:1311804/68‑1 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCAc < 1:2979571/68‑1 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:876426/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:3523871/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:3670430/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:3714086/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:2680201/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:2636549/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:1910049/1‑71 (MQ=255)
tACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt > 1:166607/1‑71 (MQ=255)
cTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCt < 1:493111/71‑1 (MQ=255)
cTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCt < 1:1324205/71‑1 (MQ=255)
cTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACtgt < 1:1847655/65‑1 (MQ=255)
cTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCtagg < 1:481314/71‑4 (MQ=255)
aTCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCTAATGACGCACTGTGCTTAgg < 1:3092344/69‑1 (MQ=255)
aTCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAgg < 1:1352079/69‑1 (MQ=255)
aTCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAgg < 1:3191785/69‑1 (MQ=255)
aTCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAgg < 1:1367587/69‑1 (MQ=255)
aCTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCa > 1:2884946/1‑71 (MQ=255)
aCTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCa > 1:382592/1‑71 (MQ=255)
aCTTCCCAGGCGATTGCTTTTGCGCCGTTTTCAAAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCa > 1:1910409/1‑71 (MQ=255)
cccAGGCGATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGAt > 1:2406273/1‑60 (MQ=255)
cccAGGCGATTACTTTTGCGCCGTTTTGACAAATGGCGAATGACGCACTGTGCTTAGGAt > 1:2406376/1‑60 (MQ=255)
gATTGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCg < 1:3007747/71‑1 (MQ=255)
tGCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGa > 1:2651799/1‑70 (MQ=255)
gCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGa > 1:723532/1‑69 (MQ=255)
gCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGa > 1:2805847/1‑69 (MQ=255)
gCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGa > 1:3372995/1‑69 (MQ=255)
gCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGa > 1:1920799/1‑69 (MQ=255)
gCTTTTGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGa > 1:1667872/1‑69 (MQ=255)
ttGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGAt > 1:3122063/1‑45 (MQ=255)
ttGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGAt > 1:1012810/1‑45 (MQ=255)
ttGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGAt > 1:533695/1‑45 (MQ=255)
gtGCGCCGTTTTCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGTACAGTc < 1:1116/69‑1 (MQ=255)
ttttCACAAATGTCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCg < 1:3434145/55‑1 (MQ=255)
ttttCACAAATGTCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCg < 1:2296648/55‑1 (MQ=255)
ttCACAAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGACAGTCAAAGCCCTCTg > 1:3651921/1‑71 (MQ=255)
caAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGACAGTCAAAGCCCTCTGGCtt < 1:3371177/71‑1 (MQ=255)
caAATGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGACAGTCAAAGCCCTCTGGCtt < 1:3007081/71‑1 (MQ=255)
aTGGCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGACAGTCAAAGCCCTCTGGCTTAt > 1:811656/1‑70 (MQ=255)
|
AGAAAGAGGCGTTTACCTGCTTATCCGTGACTTCCCAGGCGATTGCTTTTGCGCCGTTTTCACAAATGTCGAATGACGCACTGTGCTTAGGATCTGGCCATGCACAACCCGGACAGTCAAAGCCCTCTGGCTTAT > W3110S.gb/1587942‑1588076
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
