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 |
1,953,447 |
G→A |
46.0% |
A113A (GCG→GCA) |
yecE → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,953,447 | 0 | G | A | 46.0%
| 14.8
/ 64.2
| 50 | A113A (GCG→GCA) | yecE | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (17/10); new base A (9/14); total (26/24) |
| Fisher's exact test for biased strand distribution p-value = 1.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
TCCGCGCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGCCATCCA > W3110S.gb/1953384‑1953510
|
tCCGCGCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTgg > 1:4800654/1‑70 (MQ=255)
ccGCGCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCa > 1:4055647/1‑71 (MQ=255)
ccGCGCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCa > 1:2744474/1‑71 (MQ=255)
cgcgCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCa < 1:4085277/70‑1 (MQ=255)
cgcgCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCa < 1:3080273/70‑1 (MQ=255)
gcATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCAtttt > 1:2774919/1‑71 (MQ=255)
ttGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGTAGCTGCCTGCGCTTTGGCATTTtctc < 1:2894378/71‑1 (MQ=255)
ttGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTtctc < 1:4834947/71‑1 (MQ=255)
gggCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGa > 1:4090135/1‑71 (MQ=255)
gCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGAtt < 1:4576167/71‑1 (MQ=255)
cTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCtt > 1:1379817/1‑49 (MQ=255)
cTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCtt > 1:529043/1‑49 (MQ=255)
cTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTc > 1:986077/1‑71 (MQ=255)
cTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCtt > 1:416403/1‑70 (MQ=255)
cTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTc > 1:2359152/1‑71 (MQ=255)
gCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTg > 1:4116967/1‑71 (MQ=255)
tGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGc > 1:2393996/1‑71 (MQ=255)
tGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGc > 1:4960125/1‑71 (MQ=255)
tGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGc > 1:3395727/1‑71 (MQ=255)
ctgcctgcCACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAAtt > 1:1821990/1‑71 (MQ=255)
gcctgccACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAAtt > 1:2481607/1‑69 (MQ=255)
cctgccACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTaa > 1:2234728/1‑71 (MQ=255)
ccACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAAtt < 1:1887790/69‑1 (MQ=255)
ccACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAAtt < 1:3034764/69‑1 (MQ=255)
ccACATTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAAtt < 1:1585610/69‑1 (MQ=255)
caTTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGc > 1:1193895/1‑71 (MQ=255)
aTTCGGCCCACGGGAGCTGCCTGCACTTTGGCATTTtctc < 1:288242/40‑1 (MQ=255)
ttCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTtctc < 1:2527472/39‑1 (MQ=255)
ttCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGa < 1:2954302/41‑1 (MQ=255)
ttCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGa < 1:4404319/41‑1 (MQ=255)
tCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGa < 1:1496636/40‑1 (MQ=255)
tCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTg > 1:1127975/1‑71 (MQ=255)
cGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTtc > 1:313006/1‑35 (MQ=255)
ggCCCACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTgg < 1:933019/70‑1 (MQ=255)
gCCCACGGGAGCTGCCTGCGCTTTGGCATTTtctc < 1:3116591/35‑1 (MQ=255)
ccACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGt < 1:513714/71‑1 (MQ=255)
ccACGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGt < 1:853970/71‑1 (MQ=255)
cACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTaa < 1:84398/55‑1 (MQ=255)
aCGGGAGCTGCCTGCACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAAt > 1:397022/1‑55 (MQ=255)
cGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTg > 1:4066087/1‑43 (MQ=255)
cGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCg > 1:3372322/1‑71 (MQ=255)
gggAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGc > 1:1283618/1‑71 (MQ=255)
ggAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGcc < 1:4943957/71‑1 (MQ=255)
ctgcctgcACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAAtt < 1:75983/49‑1 (MQ=255)
ctgcctgcACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGCCATc < 1:4035748/70‑1 (MQ=255)
tgcctgcGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAAt < 1:4980035/47‑1 (MQ=255)
tgcctgcGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGCCATCca > 1:2711621/1‑71 (MQ=255)
cctgcGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTa > 1:648741/1‑47 (MQ=255)
ctgcACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAg < 1:4177062/57‑1 (MQ=255)
ctgcACTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAg < 1:3581179/57‑1 (MQ=255)
cgcTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGCCATcc > 1:4409480/1‑64 (MQ=255)
|
TCCGCGCATTGGGCAATACTGGCTGCAACTGCCTGCCACATTCGGCCCACGGGAGCTGCCTGCGCTTTGGCATTTTCTCGATTCTCTTCCTGGCGAATTTAATTATGGCGTGGAAGTCCGCCATCCA > W3110S.gb/1953384‑1953510
|
| 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
