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 R2
|
260 |
44.3 |
3360226 |
90.5% |
3041004 |
64.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,363,632 |
T→C |
40.0% |
F324S (TTT→TCT) |
yhcD → |
predicted outer membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,363,632 | 0 | T | C | 40.0%
| 15.0
/ 31.4
| 30 | F324S (TTT→TCT) | yhcD | predicted outer membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (3/15); new base C (5/7); total (8/22) |
| Fisher's exact test for biased strand distribution p-value = 2.10e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01 |
GTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAT > W3110S.gb/3363563‑3363690
|
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:2623280/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:996396/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:917515/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:660766/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:424908/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:3173365/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:3169406/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:3160551/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:2962549/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:2566248/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:2555788/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:2418226/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:2280487/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:1969771/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:1950176/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:1861912/1‑70 (MQ=255)
gTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGtt > 1:1815138/1‑70 (MQ=255)
ccGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:2021143/71‑1 (MQ=255)
ccGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:2223214/71‑1 (MQ=255)
ccGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:1652012/71‑1 (MQ=255)
ccGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:1180067/71‑1 (MQ=255)
ccGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:2711028/71‑1 (MQ=255)
ccGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:2811300/71‑1 (MQ=255)
cGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGaa < 1:2851614/70‑1 (MQ=255)
gTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGc > 1:1603076/1‑71 (MQ=255)
gTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGc > 1:1700107/1‑71 (MQ=255)
gTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTCTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGc > 1:252232/1‑71 (MQ=255)
gTAGTTCGCACAACTATATTGTTCCCTCCACACTGTCTAATCAGCATGt > 1:42488/1‑49 (MQ=255)
gTAGTTCGCACAACTATATTGTTCCCTACACCCTGTCTAATCAGCATGTAGAAAGCTTCCAGGGTTATCg > 1:756024/1‑70 (MQ=255)
cGCACAACTATATTGTTCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTcgc > 1:660433/1‑70 (MQ=255)
cGCACAACTATATTGTTCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTcgc > 1:1728640/1‑70 (MQ=255)
cGCACAACTATATTGTTCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTcgc > 1:3007342/1‑70 (MQ=255)
ttCCCTCCACCGTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:2887055/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:903943/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:1545253/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:970767/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:1037006/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:3293914/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:3170734/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:3110862/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:1021062/71‑1 (MQ=255)
ttCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGAc < 1:2242938/71‑1 (MQ=255)
ccTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAt < 1:2907917/71‑1 (MQ=255)
ccTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAt < 1:1529750/71‑1 (MQ=255)
ccTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAt < 1:2715936/71‑1 (MQ=255)
ccTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAt < 1:1951734/71‑1 (MQ=255)
ccTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAt < 1:1984049/71‑1 (MQ=255)
|
GTGATCTTAATGTCACCGTTGTCGAAACAGACGGTAGTTCGCACAACTATATTGTTCCCTCCACCCTGTTTAATCAGCATGTAGAAAGCTTCCAGGGTTATCGCTTCGCGATAGGGCGGGTAGACGAT > W3110S.gb/3363563‑3363690
|
| 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
