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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,311,878 |
G→A |
40.0% |
P252L (CCG→CTG) |
truB ← |
tRNA pseudouridine synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,311,878 | 0 | G | A | 40.0%
| 25.7
/ 44.8
| 40 | P252L (CCG→CTG) | truB | tRNA pseudouridine synthase |
| Reads supporting (aligned to +/- strand): ref base G (7/17); new base A (11/5); total (18/22) |
| Fisher's exact test for biased strand distribution p-value = 2.30e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.87e-01 |
CGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGT > W3110S.gb/3311821‑3311925
|
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGc > 1:574104/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGc > 1:1066116/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGc > 1:844683/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGc > 1:1769137/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGc > 1:1415271/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCAGAAg > 1:124734/1‑70 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc > 1:496119/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc > 1:763683/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc > 1:1273623/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc > 1:1317058/1‑71 (MQ=255)
cGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGc > 1:807276/1‑71 (MQ=255)
aaCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTg < 1:1024664/71‑1 (MQ=255)
aaCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTg < 1:1422949/71‑1 (MQ=255)
aaCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTg < 1:789196/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:1402386/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:1542982/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:1584285/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:1868219/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:824948/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:207440/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:210644/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:341348/71‑1 (MQ=255)
aCCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg < 1:142810/71‑1 (MQ=255)
ccGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTgg < 1:192108/70‑1 (MQ=255)
ttACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTc < 1:1162290/71‑1 (MQ=255)
aGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGt < 1:75312/71‑1 (MQ=255)
aaCAGAAGAGGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg > 1:240692/1‑71 (MQ=255)
aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg > 1:768854/1‑71 (MQ=255)
aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg > 1:1880797/1‑71 (MQ=255)
aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg > 1:1018553/1‑71 (MQ=255)
aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg > 1:1541043/1‑71 (MQ=255)
aaCAGAAGACGTTAACGGAAGATTCACCACCAGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATg > 1:1206210/1‑71 (MQ=255)
aCGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt < 1:576838/71‑1 (MQ=255)
aCGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt < 1:1382327/71‑1 (MQ=255)
aCGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt < 1:8707/71‑1 (MQ=255)
cGTTAACGTAAGATTCACCACCGGATAGTCCGAAGCTgg < 1:1079333/39‑1 (MQ=255)
cGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt < 1:702198/70‑1 (MQ=255)
cGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt < 1:282856/70‑1 (MQ=255)
gTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGt < 1:1392227/69‑1 (MQ=255)
aaCGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTaa > 1:622345/1‑56 (MQ=255)
|
CGAACCGGGTTACCATTTTTGAAGTAAACAGAAGACGTTAACGGAAGATTCACCACCGGATAGTCCGAAGCTGGACTGTCCATTGGCATCAGTAATGGATCAAGT > W3110S.gb/3311821‑3311925
|
| 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
