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 |
4,178,679 |
A→G |
40.8% |
L91S (TTA→TCA) |
gspH ← |
predicted general secretory pathway component, cryptic |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,178,679 | 0 | A | G | 40.8%
| 23.3
/ 59.3
| 49 | L91S (TTA→TCA) | gspH | predicted general secretory pathway component, cryptic |
| Reads supporting (aligned to +/- strand): ref base A (15/14); new base G (11/9); total (26/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01 |
AAGATGAATTGAGAGTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCATGCTGAATC > W3110S.gb/4178618‑4178740
|
aaGATGAATTGAGAGTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAAcc < 1:772486/70‑1 (MQ=255)
gAATTGAGAGTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAAcc < 1:866673/65‑1 (MQ=255)
gAATTGAGAGTTCTTCATCCCAGTCATTTTGGCTCTAGTCTGCGGCATCTTCTTGTAATGGAACCCAgcgc > 1:3312424/1‑71 (MQ=255)
aaTTGAGAGTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAgcgc < 1:1269215/70‑1 (MQ=255)
gagaGTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGc > 1:2765101/1‑71 (MQ=255)
agTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGa < 1:3676630/71‑1 (MQ=255)
gTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGAt < 1:3142436/71‑1 (MQ=255)
cttcATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGa > 1:4007256/1‑50 (MQ=255)
cttcATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGa > 1:3937387/1‑50 (MQ=255)
ttcATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGATgg < 1:3867459/69‑1 (MQ=255)
cATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTaa > 1:2121849/1‑43 (MQ=255)
cATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGATGGTGtt > 1:1865437/1‑71 (MQ=255)
cATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGATGGTGtt > 1:2084438/1‑71 (MQ=255)
cATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGATGGTGtt > 1:2178890/1‑71 (MQ=255)
cATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGgtg < 1:4598584/69‑1 (MQ=255)
tCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGtttt < 1:690608/71‑1 (MQ=255)
gTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCg > 1:3786456/1‑71 (MQ=255)
cATTTTGGCTCTCGTCTGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGa > 1:310131/1‑55 (MQ=255)
tttGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGttt > 1:4771209/1‑60 (MQ=255)
tttGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGttt > 1:1935881/1‑60 (MQ=255)
ttGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAAcc > 1:1565501/1‑37 (MQ=255)
ttGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCa > 1:4324519/1‑71 (MQ=255)
ttGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCa > 1:2302734/1‑71 (MQ=255)
ggCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:4918959/70‑1 (MQ=255)
ggCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:605773/70‑1 (MQ=255)
ggCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:3195425/70‑1 (MQ=255)
ctctCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGgtgt < 1:4693780/53‑1 (MQ=255)
ctcGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:3541452/66‑1 (MQ=255)
ctcGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:3547610/66‑1 (MQ=255)
ctcGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATgc > 1:302940/1‑71 (MQ=255)
ctcGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATgc > 1:1359469/1‑71 (MQ=255)
tGCGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCAt > 1:2730522/1‑70 (MQ=255)
cGGCATCTTCTTGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCAt < 1:2366005/68‑1 (MQ=255)
gCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCATGCTGa < 1:3749507/71‑1 (MQ=255)
tcttctTGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:685045/53‑1 (MQ=255)
tcttctTGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCAt < 1:993941/53‑1 (MQ=255)
tcttctTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGccc < 1:3953332/45‑1 (MQ=255)
tcttctTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGccc < 1:1180640/45‑1 (MQ=255)
cttcttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTg < 1:3172471/41‑1 (MQ=255)
cttcttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTg < 1:1092834/41‑1 (MQ=255)
ttcttGTGATGGAACCCAGCGCCAGGCTGATGGTGttt > 1:775793/1‑38 (MQ=255)
ttcttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATaa > 1:2244080/1‑53 (MQ=255)
ttcttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCATGCTGAAt > 1:1262386/1‑68 (MQ=255)
ttcttGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATaa > 1:4638304/1‑53 (MQ=255)
ttcttGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATaa > 1:1851245/1‑53 (MQ=255)
ttcttGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCATGCTGAAt > 1:3514222/1‑68 (MQ=255)
cttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGc > 1:4058923/1‑39 (MQ=255)
cttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGc > 1:2948929/1‑39 (MQ=255)
cttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGc > 1:2526379/1‑39 (MQ=255)
cttGTGATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCATGCTGAATc < 1:250179/67‑1 (MQ=255)
|
AAGATGAATTGAGAGTTCTTCATCCCAGTCATTTTGGCTCTCGTCTGCGGCATCTTCTTGTAATGGAACCCAGCGCCAGGCTGATGGTGTTTTGCCCGGTACCATAATGCGCCATGCTGAATC > W3110S.gb/4178618‑4178740
|
| 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
