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 |
3,220,824 |
C→A |
19.1% |
P235T (CCG→ACG) |
ebgR → |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,220,824 | 0 | C | A | 19.1%
| 133.6
/ 13.2
| 47 | P235T (CCG→ACG) | ebgR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base C (12/26); new base A (6/3); total (18/29) |
| Fisher's exact test for biased strand distribution p-value = 6.76e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 |
GCGCGGCGGTTTTTCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCATGAAC > W3110S.gb/3220757‑3220887
|
gcgcGGCGGTTTTTCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCg < 1:1511867/70‑1 (MQ=255)
gcgcGGCGGTTTTTCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCg < 1:1911810/70‑1 (MQ=255)
ggcggTTTTTCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAgg > 1:3955576/1‑70 (MQ=255)
gTTTTTGCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACtg > 1:658337/1‑71 (MQ=255)
gTTTTTCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACtg < 1:3544764/71‑1 (MQ=255)
tttttCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATACGAAGGCACtgt < 1:2897805/71‑1 (MQ=255)
tttCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATACGAAGGCACtgtt < 1:1045190/70‑1 (MQ=255)
ttCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACtgttt < 1:1048439/70‑1 (MQ=255)
ttCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACtgttt < 1:2284688/70‑1 (MQ=255)
ttCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACtgttt < 1:2185391/70‑1 (MQ=255)
gtcgGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTcc < 1:3645310/70‑1 (MQ=255)
gtcgGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTcc < 1:1338099/70‑1 (MQ=255)
tcgGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCtt < 1:4692655/67‑1 (MQ=255)
tcgGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCtt < 1:2273355/67‑1 (MQ=255)
tcgGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATACGAAGGCACtgtttg > 1:579065/1‑61 (MQ=255)
ttATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCg < 1:478083/43‑1 (MQ=255)
aTGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGaa > 1:4791758/1‑43 (MQ=255)
aTGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGaa > 1:4923219/1‑43 (MQ=255)
gAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAgg < 1:2151897/43‑1 (MQ=255)
gAACTGGCAAAACAAATGCTGGCGCAGGAAGACTATCCGAAgg < 1:3784070/43‑1 (MQ=255)
aaCTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCt < 1:3575754/71‑1 (MQ=255)
aCTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCa > 1:4627978/1‑43 (MQ=255)
aCTGGCAAAACAAATGCTGGCGCGGGAAGACTATACGAAGGCACt > 1:1969100/1‑45 (MQ=255)
ggCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCg > 1:120608/1‑71 (MQ=255)
ggCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCg > 1:4216451/1‑71 (MQ=255)
ggCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCg > 1:3819176/1‑71 (MQ=255)
ggCAAAACAAATGCTGGCGCGGGAAGACTATACGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCg > 1:4550013/1‑71 (MQ=255)
gCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCgg > 1:616196/1‑71 (MQ=255)
aaaaCAAATGCTGGCGCGGGAAGACTATACGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCg > 1:12337/1‑71 (MQ=255)
aaaaCAAATGCTGGCGCGGGAAGACTATACGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCg > 1:220969/1‑71 (MQ=255)
aaaaCAAATGCTCGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCg < 1:343382/71‑1 (MQ=255)
aaaCAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGt < 1:3169307/71‑1 (MQ=255)
aaCAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTa > 1:26253/1‑71 (MQ=255)
aCAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTAc > 1:3697010/1‑71 (MQ=255)
aCAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTAc > 1:779243/1‑71 (MQ=255)
cAAATGCTGGCGCGGGAAGACTATACGAAGGCACTGTTTGTTGCTTCCGATTCCa > 1:220676/1‑55 (MQ=255)
cTGGCGCTGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGc < 1:785976/71‑1 (MQ=255)
gcgcGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAAt < 1:2032743/71‑1 (MQ=255)
cgGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCa < 1:5105240/71‑1 (MQ=255)
cgGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCa < 1:4077121/71‑1 (MQ=255)
cgGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCa < 1:650218/71‑1 (MQ=255)
gggAAGACTATACGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCAt < 1:1835977/71‑1 (MQ=255)
aGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCATGAAc < 1:4441759/71‑1 (MQ=255)
tCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGc < 1:535179/36‑1 (MQ=255)
tCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCATg < 1:4481582/62‑1 (MQ=255)
tCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCATg < 1:4795249/62‑1 (MQ=255)
tCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGAGTACTGCGGGCAATTCATg < 1:2400842/62‑1 (MQ=255)
|
GCGCGGCGGTTTTTCCAGTTCGTCGGGTTATGAACTGGCAAAACAAATGCTGGCGCGGGAAGACTATCCGAAGGCACTGTTTGTTGCTTCCGATTCCATTGCTATCGGCGTACTGCGGGCAATTCATGAAC > W3110S.gb/3220757‑3220887
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
