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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,823,871 |
A→G |
38.6% |
intergenic (+616/+342) |
nrfG → / ← pheU |
heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,823,871 | 0 | A | G | 38.6%
| 38.4
/ 58.8
| 57 | intergenic (+616/+342) | nrfG/pheU | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
| Reads supporting (aligned to +/- strand): ref base A (18/17); new base G (16/6); total (34/23) |
| Fisher's exact test for biased strand distribution p-value = 1.66e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.39e-01 |
CCAAAGAAAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCA > minE/2823804‑2823936
|
ccAAAGAAAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGAttgtta < 1:1191954/71‑1 (MQ=255)
aaaGAAAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAg > 1:3555943/1‑70 (MQ=255)
aaGAAAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTc > 1:1664991/1‑71 (MQ=255)
aaaaaTGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGattgtt < 1:587110/64‑1 (MQ=255)
aTGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCAt < 1:2946415/71‑1 (MQ=255)
tCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAg > 1:2810178/1‑70 (MQ=255)
cAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGc > 1:2270054/1‑70 (MQ=255)
cAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGc > 1:2604189/1‑64 (MQ=255)
aGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCaa < 1:3201320/71‑1 (MQ=255)
aaaaTAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGc > 1:447329/1‑71 (MQ=255)
aaaaTAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGc > 1:3521127/1‑71 (MQ=255)
aaaTAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTTATGGATTGTTAGTCTTTGCATGAGCAAGc > 1:956394/1‑70 (MQ=255)
aaaTAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCg < 1:2227654/71‑1 (MQ=255)
aataatCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGc > 1:33897/1‑65 (MQ=255)
tCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa < 1:969312/71‑1 (MQ=255)
aaaTTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACAttt > 1:3016185/1‑70 (MQ=255)
aaTTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGa < 1:1737794/49‑1 (MQ=255)
aaTTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACAt > 1:1146506/1‑67 (MQ=255)
aaTTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTtct > 1:3196758/1‑71 (MQ=255)
aTTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTtctc > 1:834936/1‑71 (MQ=255)
ttGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAg > 1:2704371/1‑48 (MQ=255)
ttGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTctct > 1:173012/1‑71 (MQ=255)
tCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTg < 1:769086/71‑1 (MQ=255)
tCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTg > 1:253791/1‑71 (MQ=255)
cGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTtc < 1:1689639/63‑1 (MQ=255)
cGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGt > 1:627057/1‑70 (MQ=255)
ggAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGc > 1:2676781/1‑43 (MQ=255)
gAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTtct > 1:555489/1‑71 (MQ=255)
aGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCaa > 1:2174967/1‑43 (MQ=255)
aGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCaa > 1:3731398/1‑43 (MQ=255)
aGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTtctc < 1:2313931/71‑1 (MQ=255)
gCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCa > 1:2969233/1‑71 (MQ=255)
aCTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa > 1:2385646/1‑49 (MQ=255)
tACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTtctc < 1:3585582/65‑1 (MQ=255)
tACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTctct > 1:820230/1‑57 (MQ=255)
tACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCAtt > 1:1170533/1‑68 (MQ=255)
aCTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAg > 1:1656729/1‑70 (MQ=255)
cTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGa < 1:2535014/70‑1 (MQ=255)
tATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTg > 1:2240167/1‑57 (MQ=255)
tATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCttt > 1:813790/1‑56 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTtctc < 1:2924523/51‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTtctc < 1:179103/51‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGaaa < 1:1757529/69‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAt > 1:1665334/1‑71 (MQ=255)
ttttAATGGATTATTAATCTTTGCATATTCAAATGGACTGATAAACCTTTCTCTGTTTACATCCAGAAAAt < 1:2590826/71‑1 (MQ=255)
ttttAATGGATTATTAATCTTTGCATATTCAAATGGACTGATAAACCTTTCTCTGTTTACATCCAGAAAAt < 1:3882836/71‑1 (MQ=255)
ttttAATGGATTATTAATCTTTGCATATTCAAATGGACTGATAAACCTTTCTCTGTTTACATCCAGAAAAt < 1:609515/71‑1 (MQ=255)
ttAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGaa > 1:2417342/1‑66 (MQ=255)
ttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtct > 1:1467178/1‑71 (MQ=255)
ttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtc < 1:861257/70‑1 (MQ=255)
ttAATGGATTATTAATCTTTGCATATTCAAATGGACTGATAAACCTTTCTCTGTTTACATCCAGaaaa > 1:1024546/1‑68 (MQ=255)
tAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtct > 1:407663/1‑70 (MQ=255)
tAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtct > 1:2831932/1‑70 (MQ=255)
aaTGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtctc < 1:3772099/70‑1 (MQ=255)
aTGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtctc < 1:2137625/69‑1 (MQ=255)
aTGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcat < 1:575987/71‑1 (MQ=255)
aTGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcat < 1:2063210/71‑1 (MQ=255)
gATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcatca < 1:2703510/70‑1 (MQ=255)
gATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcatca < 1:2491015/70‑1 (MQ=255)
attgttAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGt < 1:229110/47‑1 (MQ=255)
ttattaGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTtc > 1:670358/1‑48 (MQ=255)
tattaGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtct < 1:547262/62‑1 (MQ=255)
|
CCAAAGAAAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCA > minE/2823804‑2823936
|
| 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
