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 |
2,773,435 |
T→C |
78.7% |
L488L (TTG→CTG) |
yfjW → |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,773,435 | 0 | T | C | 78.7%
| 130.8
/ 30.1
| 61 | L488L (TTG→CTG) | yfjW | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (8/5); new base C (14/34); total (22/39) |
| Fisher's exact test for biased strand distribution p-value = 4.96e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTT > W3110S.gb/2773367‑2773495
|
aGTTTAGTATCAACGGGAAACATTTGTCGTTTAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:615546/71‑1 (MQ=255)
ttAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTAt > 1:1125743/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg > 1:606776/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg > 1:293239/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg > 1:1909712/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg > 1:1868395/1‑71 (MQ=255)
tAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATg > 1:611040/1‑71 (MQ=255)
tATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:2051597/64‑1 (MQ=255)
tATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:3160871/64‑1 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGAc > 1:2188748/1‑69 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGAc > 1:3331964/1‑69 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGAc > 1:19011/1‑69 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa < 1:2229893/64‑1 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa < 1:394295/64‑1 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGAc > 1:3236374/1‑69 (MQ=255)
tCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGAc > 1:3667302/1‑69 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:406893/1‑62 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:1745154/1‑62 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa > 1:2203253/1‑62 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGt > 1:1970166/1‑71 (MQ=255)
aaCGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGt > 1:3323960/1‑71 (MQ=255)
aaaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:1189575/54‑1 (MQ=255)
aaaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:812267/54‑1 (MQ=255)
aaaCATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:878017/54‑1 (MQ=255)
cATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTtaataa > 1:2629256/1‑68 (MQ=255)
tttGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTa < 1:1343398/51‑1 (MQ=255)
tCGTTAAGGCCAGAATCGGAGATTATTATTTGTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaa < 1:343909/71‑1 (MQ=255)
tCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATg < 1:28245/49‑1 (MQ=255)
tCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCaaaaa < 1:1042096/71‑1 (MQ=255)
ttAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACt < 1:672172/50‑1 (MQ=255)
ttAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACt < 1:2973465/50‑1 (MQ=255)
ttAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACt < 1:2481403/50‑1 (MQ=255)
ttAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACt < 1:2096241/50‑1 (MQ=255)
ttAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:834569/42‑1 (MQ=255)
ttAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTCTg < 1:2383201/42‑1 (MQ=255)
cAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTATTTAATAAAAGCAAAAAAATCAAAata < 1:3523341/71‑1 (MQ=255)
cAGAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAata < 1:3296752/71‑1 (MQ=255)
aGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatat < 1:3681767/71‑1 (MQ=255)
gAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatata < 1:2613848/71‑1 (MQ=255)
gAATCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAatata < 1:3301897/71‑1 (MQ=255)
tCGGAGATTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATgg < 1:1227120/71‑1 (MQ=255)
gagaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcag < 1:2958376/71‑2 (MQ=255)
gagaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:3229120/71‑1 (MQ=255)
gagaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:1479731/71‑1 (MQ=255)
gagaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:457680/71‑1 (MQ=255)
gaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcag > 1:3455607/1‑71 (MQ=255)
gaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcag > 1:2739313/1‑71 (MQ=255)
gaTTATTATTTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcag > 1:1685974/1‑71 (MQ=255)
attattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAat < 1:1230521/59‑1 (MQ=255)
attattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:673120/68‑1 (MQ=255)
attattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:1858155/68‑1 (MQ=255)
attattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:2540197/68‑1 (MQ=255)
ttattattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGcac < 1:996482/67‑1 (MQ=255)
attattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcag > 1:398605/1‑67 (MQ=255)
attattTCTGAAGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCAcag > 1:2057367/1‑67 (MQ=255)
aaGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGttt < 1:1954078/69‑1 (MQ=255)
aGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:39295/42‑1 (MQ=255)
aGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:3705004/42‑1 (MQ=255)
aGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:2242720/42‑1 (MQ=255)
aGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:1253942/42‑1 (MQ=255)
aGGGAGTCTGTATGGACTAGTTAATAAAAGCAAAAAAATCaa < 1:112399/42‑1 (MQ=255)
|
AGTTTAGTATCAACGGGAAACATTTGTCGTTAAGGCCAGAATCGGAGATTATTATTTCTGAAGGGAGTTTGTATGGACTAGTTAATAAAAGCAAAAAAATCAAAATATATGGCACAGCAGATCTTGTTT > W3110S.gb/2773367‑2773495
|
| 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
