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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,663,570 |
Δ1 bp |
22.9% |
coding (552/882 nt) |
yfhR → |
predicted peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,663,570 | 0 | T | . | 22.9%
| 99.2
/ 36.9
| 48 | coding (552/882 nt) | yfhR | predicted peptidase |
| Reads supporting (aligned to +/- strand): ref base T (20/17); new base . (7/4); total (27/21) |
| Fisher's exact test for biased strand distribution p-value = 7.33e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.45e-01 |
CGGGCAGAGTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGATCCCCGGC > W3110S.gb/2663504‑2663633
|
cGGGCAGAGTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCgg > 1:3362206/1‑71 (MQ=255)
ggCAGAGTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTg < 1:1720418/71‑1 (MQ=255)
cAGAGTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGATc < 1:3431856/71‑1 (MQ=255)
gagTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATcc > 1:658972/1‑71 (MQ=255)
agTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGATCCTc < 1:2471410/71‑1 (MQ=255)
gTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGAACGTGAAGGCATACGTGCGGTGATCCTc < 1:1481158/71‑1 (MQ=255)
tATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTc < 1:334406/70‑1 (MQ=255)
ttGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCgg > 1:1210449/1‑60 (MQ=255)
gCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATc > 1:1595359/1‑57 (MQ=255)
gCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGATCCTCGa > 1:132096/1‑61 (MQ=255)
gCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGATCCTCGACTCCACAttt < 1:2104256/71‑1 (MQ=255)
cGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACAttt < 1:3018642/71‑1 (MQ=255)
cGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACAttt < 1:2315452/71‑1 (MQ=255)
gAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGAt > 1:1017778/1‑53 (MQ=255)
gAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGAt > 1:1011597/1‑53 (MQ=255)
aaTATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGc < 1:2176987/47‑1 (MQ=255)
tatTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGa < 1:4049340/50‑1 (MQ=255)
tatTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCct > 1:3442082/1‑71 (MQ=255)
ttCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCctct < 1:1843502/71‑1 (MQ=255)
ttCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACG‑GCGGTGATCCTCGACTCCACATTTGCctct > 1:1715283/1‑70 (MQ=255)
tCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCcaca > 1:2532102/1‑61 (MQ=255)
cTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTa > 1:717059/1‑71 (MQ=255)
cTGGATGTTATTGGTCGGGGTGATAGTGAAGGCATACG‑GCGGTGATCCTCGACTCCACATTTGCCTCtt > 1:767536/1‑69 (MQ=255)
gATGGTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTAt < 1:926100/69‑1 (MQ=255)
ttATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGt < 1:2348160/37‑1 (MQ=255)
ttATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGt < 1:1262465/37‑1 (MQ=255)
ttATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTg < 1:3496193/38‑1 (MQ=255)
tATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGAc > 1:3912301/1‑46 (MQ=255)
aTTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGAt > 1:4188426/1‑38 (MQ=255)
aTTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTa > 1:1249214/1‑62 (MQ=255)
ggTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAAc < 1:1870028/65‑1 (MQ=255)
ggTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGc > 1:1410193/1‑71 (MQ=255)
gTCGGGGTGATCGTGAAGGCATACG‑GCGGTGATCCTCGa > 1:2332967/1‑39 (MQ=38)
aTCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCtt > 1:986041/1‑48 (MQ=255)
aTCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCtt > 1:3909642/1‑48 (MQ=255)
aTCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAAt > 1:3389120/1‑70 (MQ=255)
tCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTa < 1:1240864/48‑1 (MQ=255)
cGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCaa > 1:4172154/1‑52 (MQ=255)
cGTGAAGGCATACG‑GCGGTGATACTCGACTCCACATTTGCCTCTTa > 1:1616795/1‑46 (MQ=38)
tGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAAcc < 1:2734360/52‑1 (MQ=255)
gAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATg > 1:753870/1‑46 (MQ=255)
gCATACG‑GCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGATCCCCGGc < 1:4086088/70‑1 (MQ=255)
cATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGATCCCCg > 1:4015709/1‑68 (MQ=255)
tACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCa < 1:1071288/41‑1 (MQ=255)
tACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGAt < 1:4106874/61‑1 (MQ=255)
aCGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGAt > 1:3918189/1‑60 (MQ=255)
aCGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGAt > 1:2581284/1‑60 (MQ=255)
gTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGccaa > 1:4361896/1‑49 (MQ=255)
|
CGGGCAGAGTATTGGCGGGGCGAATATTCTGGATGTTATTGGTCGGGGTGATCGTGAAGGCATACGTGCGGTGATCCTCGACTCCACATTTGCCTCTTATGCAACCATCGCCAACCAAATGATCCCCGGC > W3110S.gb/2663504‑2663633
|
| 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
