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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,530,607 |
G→A |
12.5% |
T69I (ACT→ATT) |
yfcA ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,530,607 | 0 | G | A | 12.5%
| 108.9
/ 6.8
| 40 | T69I (ACT→ATT) | yfcA | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base G (15/20); new base A (2/3); total (17/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.36e-01 |
GACAAAGGTCATGGCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGGAGACATCCCC > minE/1530537‑1530675
|
gACAAAGGTCATGGCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGAtag < 1:2839174/71‑1 (MQ=255)
aaaGGTCATGGCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGAtagtag > 1:2740889/1‑71 (MQ=255)
aTGGCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGaaa < 1:4073022/70‑1 (MQ=255)
gCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATag < 1:1977031/70‑1 (MQ=255)
gCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATag < 1:2877735/70‑1 (MQ=255)
gATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAgc > 1:766009/1‑71 (MQ=255)
atTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAATAGCGGAAATAGAgccgc > 1:2351308/1‑71 (MQ=255)
ttGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAgccgcc > 1:4115542/1‑71 (MQ=255)
tGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGccgccg > 1:994693/1‑71 (MQ=255)
aGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCa < 1:1402535/71‑1 (MQ=255)
tttCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGa < 1:3427675/54‑1 (MQ=255)
tttCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAgg < 1:1273653/71‑1 (MQ=255)
tCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGccgccg > 1:3757661/1‑65 (MQ=255)
tCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGc < 1:2580823/70‑1 (MQ=255)
tCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCt > 1:1199481/1‑71 (MQ=255)
cTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCt < 1:361589/70‑1 (MQ=255)
aTCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAATAGCGGAAATAGAGCCGCCGCAGGCTTGCa < 1:3814819/71‑1 (MQ=255)
cGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGt > 1:340924/1‑71 (MQ=255)
cTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGttt < 1:1183610/71‑1 (MQ=255)
aaaCTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTa < 1:2866013/69‑1 (MQ=255)
aaaCTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTAt > 1:2236372/1‑70 (MQ=255)
aaCTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTg > 1:1910739/1‑71 (MQ=255)
cTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGa < 1:544958/38‑1 (MQ=255)
aCCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGc < 1:927106/71‑1 (MQ=255)
aCCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGc < 1:2112482/71‑1 (MQ=255)
aCCACTTTGCGGCGAATAAAGTAGATAATAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGc > 1:736483/1‑71 (MQ=255)
tGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCa > 1:43788/1‑71 (MQ=255)
cggcgAATAAAGTAGATAATAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCAtt < 1:3494863/71‑1 (MQ=255)
gccgAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCa < 1:2075494/66‑1 (MQ=255)
cgAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGc > 1:4063625/1‑71 (MQ=255)
gAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTAt < 1:2935391/51‑1 (MQ=255)
gAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTAt < 1:886421/51‑1 (MQ=255)
gAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTAt < 1:679287/51‑1 (MQ=255)
aaTAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCgg > 1:943549/1‑71 (MQ=255)
aTAAAGTAGATAATAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCgg < 1:1888395/70‑1 (MQ=255)
tAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCt < 1:2909729/38‑1 (MQ=255)
tAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCgg > 1:2439780/1‑69 (MQ=255)
tAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGga < 1:142346/71‑1 (MQ=255)
aaGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGc > 1:3354542/1‑65 (MQ=255)
aGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGgaga > 1:3944371/1‑70 (MQ=255)
aGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGgaga > 1:3561607/1‑70 (MQ=255)
gTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGGAGACa < 1:1985450/71‑1 (MQ=255)
tagtagCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGGAGACATcccc > 1:617145/1‑71 (MQ=255)
agtagCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGc < 1:2695527/45‑1 (MQ=255)
|
GACAAAGGTCATGGCGATATTGAGTTTCTGATCGCTTAAACTAACCACTTTGCGGCGAATAAAGTAGATAGTAGCGGAAATAGAGCCGCCGCAGGCTTGCAGTTTATTGGTTGCCAGCGCATTAGCGGGAGACATCCCC > minE/1530537‑1530675
|
| 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
