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 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,761,776 |
C→T |
L154L (CTG→CTA) |
sufS ← |
selenocysteine lyase, PLP‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,761,776 | 0 | C | T | 88.9%
| 99.3
/ 4.6
| 36 | L154L (CTG→CTA) | sufS | selenocysteine lyase, PLP‑dependent |
| Reads supporting (aligned to +/- strand): ref base C (0/4); new base T (24/8); total (24/12) |
| Fisher's exact test for biased strand distribution p-value = 8.40e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
AGACATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGC > W3110S.gb/1761718‑1761837
|
agaCATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTa < 1:1084851/71‑1 (MQ=255)
agaCATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTa < 1:1837103/71‑1 (MQ=255)
agaCATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTa < 1:2479574/71‑1 (MQ=255)
gTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCgg < 1:954711/70‑1 (MQ=255)
tAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGa < 1:3681152/71‑1 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAg > 1:3638162/1‑71 (MQ=255)
gcagGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCggg < 1:881079/71‑1 (MQ=255)
gcagGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCggg < 1:2893540/71‑1 (MQ=255)
gcagGCGAGTTCTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCggg < 1:3744440/71‑1 (MQ=255)
agGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCggg < 1:2745965/69‑1 (MQ=255)
gCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGa < 1:616734/58‑1 (MQ=255)
gAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGAt > 1:964161/1‑67 (MQ=255)
gAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATcaca > 1:1370135/1‑71 (MQ=255)
gAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATcaca > 1:319225/1‑71 (MQ=255)
gAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATcaca > 1:2937779/1‑71 (MQ=255)
gAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATcaca > 1:1602249/1‑71 (MQ=255)
gAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTATAGTTGCAACGTACCATCGGGATTGAGCGGGATcaca > 1:3788321/1‑71 (MQ=255)
gAGTTATCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATcac > 1:673874/1‑70 (MQ=255)
ctcATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCatc < 1:3173912/70‑3 (MQ=255)
caAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTgcg > 1:1514602/1‑71 (MQ=255)
caAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTgcg > 1:3246810/1‑71 (MQ=255)
caAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTgcg > 1:1857788/1‑71 (MQ=255)
caAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTgc > 1:162056/1‑70 (MQ=255)
aCAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTgcgc > 1:1913685/1‑69 (MQ=255)
aCAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGcc > 1:3641723/1‑70 (MQ=255)
tAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGa < 1:2271193/35‑1 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAg > 1:2190313/1‑39 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTgcg > 1:457745/1‑61 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:3435515/1‑71 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:1746598/1‑71 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:3246090/1‑71 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:1937825/1‑71 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:2840926/1‑71 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:2458646/1‑71 (MQ=255)
aGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:2351068/1‑71 (MQ=255)
aGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgcgc > 1:1981570/1‑70 (MQ=255)
|
AGACATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGC > W3110S.gb/1761718‑1761837
|
| 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
