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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
345,099 |
C→T |
25.0% |
A155T (GCC→ACC) |
yahN ← |
neutral amino‑acid efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 345,099 | 0 | C | T | 25.0%
| 97.2
/ 31.7
| 52 | A155T (GCC→ACC) | yahN | neutral amino‑acid efflux system |
| Reads supporting (aligned to +/- strand): ref base C (19/20); new base T (7/6); total (26/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGT > W3110S.gb/345033‑345162
|
gCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTAtt > 1:477671/1‑70 (MQ=255)
gCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAttt < 1:4066861/71‑1 (MQ=255)
gCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAtt > 1:320369/1‑70 (MQ=255)
gCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAtt > 1:2554300/1‑70 (MQ=255)
tAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAAt > 1:4200586/1‑68 (MQ=255)
aaTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTaa > 1:479061/1‑66 (MQ=255)
aaTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTaa > 1:867747/1‑66 (MQ=255)
aaTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTaa > 1:2129154/1‑66 (MQ=255)
aTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCAt > 1:4073042/1‑61 (MQ=255)
aTTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCAGGTTGGTGTTTCGGCAt > 1:1597549/1‑61 (MQ=255)
aTTGATGCGAGCACAATCCCCGCCAAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTaa > 1:4693091/1‑65 (MQ=255)
gATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTg < 1:4190380/70‑1 (MQ=255)
gCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATg < 1:3081367/57‑1 (MQ=255)
cacaATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCa > 1:4318615/1‑49 (MQ=255)
ccccGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGa > 1:1597120/1‑68 (MQ=255)
cccAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATaaaaaa > 1:2916828/1‑70 (MQ=255)
cAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACTGATAAAAAATaa < 1:4027850/71‑1 (MQ=255)
ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGtt < 1:3235935/38‑1 (MQ=255)
ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa < 1:1431492/48‑1 (MQ=255)
ttAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa < 1:1406206/48‑1 (MQ=255)
aaaCGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATAc < 1:1788206/49‑1 (MQ=255)
aaaCGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATAc < 1:4997221/49‑1 (MQ=255)
aaaCGTGCCCATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATACTGATAAAAAATaaa > 1:1992556/1‑63 (MQ=255)
aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTa > 1:4967696/1‑37 (MQ=255)
aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa > 1:338203/1‑46 (MQ=255)
aaaCGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa > 1:2318622/1‑46 (MQ=255)
cccATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGtt < 1:2672274/70‑1 (MQ=255)
ccATGTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATa > 1:1338459/1‑40 (MQ=255)
tGTTGGTGTTTCTGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTg < 1:2260211/60‑1 (MQ=255)
tGTTGGTGTTTCGGCATTTAATGTTACTGAGaaaa > 1:1353266/1‑35 (MQ=255)
tGTTGGAGTTTCGGCATTTAATGTTCCTGAGaaaa < 1:1635695/35‑1 (MQ=37)
gTTGGTGTTTCGGTATTTAATGTTACTGAGAAAATAc < 1:902017/37‑1 (MQ=255)
gTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaaaa < 1:808829/52‑1 (MQ=255)
gTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaaaa < 1:398524/52‑1 (MQ=255)
gTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCggg > 1:3701268/1‑63 (MQ=255)
ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATaaaa > 1:3035014/1‑51 (MQ=255)
ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCgg > 1:2904485/1‑61 (MQ=255)
ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCgg > 1:4761829/1‑61 (MQ=255)
ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTagagag < 1:3334213/70‑1 (MQ=255)
ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga > 1:4537621/1‑67 (MQ=255)
ttGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAgagaga < 1:1508736/71‑1 (MQ=255)
tgtTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGc < 1:383542/55‑1 (MQ=255)
tgtTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTaga < 1:2432669/63‑1 (MQ=255)
tttCGGTATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGt < 1:4966714/70‑1 (MQ=255)
tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCg < 1:1646244/54‑1 (MQ=255)
tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGAt < 1:3089128/66‑1 (MQ=255)
tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGt < 1:993403/70‑1 (MQ=255)
tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGt < 1:1031045/70‑1 (MQ=255)
tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGt < 1:2116657/70‑1 (MQ=255)
tttCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGt < 1:1037025/70‑1 (MQ=255)
tCGGTATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTa > 1:341397/1‑57 (MQ=255)
tCGGCATTTAATGTTACTGAGAAAATACTGATaaa > 1:605034/1‑35 (MQ=255)
|
GCCAGATAATTGATGCGAGCACAATCCCCGCCCAGGCCATTAAACGTGCCCATGTTGGTGTTTCGGCATTTAATGTTACTGAGAAAATACTGATAAAAAATAAAACGGTTTGCGGGTTAGAGAGATCGGT > W3110S.gb/345033‑345162
|
| 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
