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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,348,627 |
C→A |
21.9% |
intergenic (+147/+234) |
yihA → / ← polA |
GTP‑binding protein/fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,348,627 | 0 | C | A | 21.9%
| 111.6
/ 13.2
| 41 | intergenic (+147/+234) | yihA/polA | GTP‑binding protein/fused DNA polymerase I 5'‑>3' exonuclease, 3'‑>5' polymerase and 3'‑>5' exonuclease |
| Reads supporting (aligned to +/- strand): ref base C (20/12); new base A (7/2); total (27/14) |
| Fisher's exact test for biased strand distribution p-value = 6.92e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01 |
CTGATAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGATAGAACATC > minE/2348558‑2348697
|
cTGATAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTact < 1:3536863/71‑1 (MQ=255)
cTGATAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTact < 1:2703571/71‑1 (MQ=255)
cTGATAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTact < 1:2601438/71‑1 (MQ=255)
cTGATAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTact < 1:1841222/71‑1 (MQ=255)
aTAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTactg < 1:2250018/69‑1 (MQ=255)
tAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTactgact > 1:3589186/1‑71 (MQ=255)
tAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTactgact > 1:2792725/1‑71 (MQ=255)
tAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTactgact > 1:688833/1‑71 (MQ=255)
tAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTactga < 1:3310633/69‑1 (MQ=255)
aTAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGggc < 1:2966399/71‑1 (MQ=255)
aGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGggcgg > 1:416496/1‑71 (MQ=255)
cgcATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTact < 1:1542244/58‑1 (MQ=255)
gcATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCt > 1:1299640/1‑70 (MQ=255)
aGGCATTACGGATCTTTTCTTTCGCCCAATAAAACACGCCCCAGTCATTact < 1:3108506/52‑1 (MQ=255)
aGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAata > 1:3022593/1‑71 (MQ=255)
aTTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATAtt > 1:1644519/1‑69 (MQ=255)
aTTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATAtt > 1:4226933/1‑69 (MQ=255)
aCGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTactgact > 1:1353989/1‑49 (MQ=255)
gtaTCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAata < 1:129946/60‑1 (MQ=255)
cttttctttCGCCCAATAAAAAACGCCCCAGTCATTactg < 1:1459036/40‑1 (MQ=255)
tctttcGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGAt < 1:745214/70‑1 (MQ=255)
ctttcGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTaaaa > 1:2117871/1‑51 (MQ=255)
ctttcGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTaaaa > 1:2624203/1‑51 (MQ=255)
gCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTg < 1:158272/70‑1 (MQ=255)
ccAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACTTg < 1:1388208/68‑1 (MQ=255)
aTAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTaa < 1:1222784/71‑1 (MQ=255)
tAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTaa > 1:2610222/1‑70 (MQ=255)
aaaaaCGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAg > 1:3568690/1‑71 (MQ=255)
aaaCGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGt < 1:4187158/71‑1 (MQ=255)
aaCGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTc < 1:1235500/71‑1 (MQ=255)
cccAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGaaa < 1:1025740/71‑1 (MQ=255)
cccAGTCAGTAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGaaa < 1:4096043/71‑1 (MQ=255)
cccAGTCAGTAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGaaa < 1:3235329/71‑1 (MQ=255)
ccAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAg < 1:269266/71‑1 (MQ=255)
ccAGTCAGTAATGACTGGGGCGGCTAAAATATTCCGCCAAATCCGATTACGGGAAGTAAAAGGTCTGa > 1:1434107/1‑68 (MQ=37)
ccAGTCAGTAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGa > 1:1428931/1‑68 (MQ=255)
ccAGTCAGTAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGa > 1:1293185/1‑68 (MQ=255)
cagtcagtAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCt > 1:3712635/1‑65 (MQ=255)
cagtcagtAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTg > 1:3717446/1‑66 (MQ=255)
cagtcagtAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGa > 1:89177/1‑67 (MQ=255)
cagtcagtAATGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGa > 1:1476302/1‑67 (MQ=255)
cAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGTAGTAAAAGGTCTGa > 1:3674740/1‑67 (MQ=255)
cAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTg > 1:2432140/1‑66 (MQ=255)
cAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGa > 1:3156637/1‑67 (MQ=255)
cAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGa > 1:3669804/1‑67 (MQ=255)
gTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTaaaa > 1:199846/1‑58 (MQ=255)
gTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTaaaa > 1:570585/1‑58 (MQ=255)
aTTACTGACTGTGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGa > 1:3824692/1‑66 (MQ=255)
aTTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGa > 1:2576747/1‑66 (MQ=255)
aTTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGa > 1:188879/1‑66 (MQ=255)
aTTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGa > 1:3551007/1‑66 (MQ=255)
aTTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGATAGaa > 1:59545/1‑71 (MQ=255)
ttACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTg < 1:108294/46‑1 (MQ=255)
ttACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGATAGAAc < 1:850766/71‑1 (MQ=255)
actgactgGGGCGGCT‑AAATATTCAGCCAAATCCGATTACGTGaa > 1:3935966/1‑45 (MQ=255)
ctgactgGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGATAGAACATc > 1:3140128/1‑71 (MQ=255)
ctgactgGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGATAGAACATc > 1:777695/1‑71 (MQ=255)
|
CTGATAAACATAGCGCATCAGGCATTACGGATCTTTTCTTTCGCCCAATAAAAAACGCCCCAGTCATTACTGACTGGGGCGGCTAAAATATTCAGCCAAATCCGATTACGTGAAGTAAAAGGTCTGAAAGATAGAACATC > minE/2348558‑2348697
|
| 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
