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 |
2,823,871 |
A→G |
34.9% |
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 | 34.9%
| 60.4
/ 62.2
| 63 | 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 (15/26); new base G (11/11); total (26/37) |
| Fisher's exact test for biased strand distribution p-value = 4.21e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
AAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCAGT > minE/2823811‑2823938
|
aaaaTGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTg < 1:3252171/71‑1 (MQ=255)
aaaaTGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTg < 1:2785730/71‑1 (MQ=255)
aaaTGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGc < 1:3122313/71‑1 (MQ=255)
cAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGc > 1:2897820/1‑70 (MQ=255)
aGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCa < 1:2670419/70‑1 (MQ=255)
aaaTAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCg < 1:1632918/71‑1 (MQ=255)
aataatCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGa < 1:1813912/71‑1 (MQ=255)
tGGAAAATTGTCCTGAGCACTTACTATTTTAATGGATTATTAGTc < 1:2068250/45‑1 (MQ=255)
gAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACAtt > 1:935496/1‑71 (MQ=255)
gAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACAtt > 1:4105579/1‑71 (MQ=255)
gAAAATTGTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACAtt > 1:1257557/1‑71 (MQ=255)
gAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGa > 1:2310077/1‑52 (MQ=255)
gAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACAtt > 1:113030/1‑71 (MQ=255)
gAAAATAGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGa > 1:539873/1‑52 (MQ=255)
aTTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTtctc < 1:1487202/71‑1 (MQ=255)
tGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCtt > 1:297748/1‑71 (MQ=255)
gTCCGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCAt > 1:3226369/1‑43 (MQ=255)
tCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTg < 1:3493600/71‑1 (MQ=255)
ccGGAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTg > 1:1625107/1‑70 (MQ=255)
cGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGa > 1:3962235/1‑42 (MQ=255)
cGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCttt < 1:3095038/68‑1 (MQ=255)
cGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGtt > 1:1469610/1‑71 (MQ=255)
ggAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCtt < 1:2916013/66‑1 (MQ=255)
ggAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGa < 1:3023725/49‑1 (MQ=255)
ggAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTtc < 1:1032707/71‑1 (MQ=255)
gAGCACTTACTATTTTAATGGATTGTTAGTCTTTGCAt < 1:3026155/38‑1 (MQ=255)
gAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTtct < 1:4023132/71‑1 (MQ=255)
gCACTTACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCa > 1:1206669/1‑71 (MQ=255)
cTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGaa > 1:3119468/1‑44 (MQ=255)
ttACTATTTTAATGGATTGTTAGTCTTTGCATGAGCa < 1:2847175/37‑1 (MQ=255)
ttACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAgag < 1:1695497/41‑3 (MQ=255)
ttACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCg < 1:1115706/41‑1 (MQ=255)
ttACTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCAtt > 1:2451593/1‑69 (MQ=255)
ttACTATTTTAATGGATTATTAGTCTTTGCATGAGCa < 1:1287468/37‑1 (MQ=255)
ttACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa < 1:2621874/47‑1 (MQ=255)
ttACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa < 1:360704/47‑1 (MQ=255)
ttACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa < 1:1945963/47‑1 (MQ=255)
tACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCtt < 1:2306150/58‑1 (MQ=255)
aCTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCa > 1:704261/1‑69 (MQ=255)
aCTATTTTAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAg > 1:3155230/1‑70 (MQ=255)
aCTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAg > 1:1938506/1‑70 (MQ=255)
aCTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAg > 1:696225/1‑70 (MQ=255)
cTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa > 1:4091320/1‑44 (MQ=255)
cTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGa > 1:253670/1‑44 (MQ=255)
aTTTTAATGGATTATTAGTCTTTGCATGAGCAAGCg < 1:2258078/36‑1 (MQ=255)
ttttAATGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTctct < 1:544870/52‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCg < 1:1111254/35‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACAt < 1:2225576/46‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGaaa < 1:342800/69‑1 (MQ=255)
ttttAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGaaa < 1:4101150/69‑1 (MQ=255)
ttAATGGATTGTTAGTCTTTGCATGAGCAAGCTaa > 1:2423822/1‑35 (MQ=38)
tAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGaaaa > 1:3747606/1‑67 (MQ=255)
tAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtct < 1:2793272/70‑1 (MQ=255)
caTGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACAttt > 1:1747821/2‑44 (MQ=255)
aaTGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAAtctc < 1:2343694/70‑1 (MQ=255)
aTGGATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcat < 1:720501/71‑1 (MQ=255)
aTGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcat < 1:197432/71‑1 (MQ=255)
tGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACAttt < 1:1751292/42‑1 (MQ=255)
tGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACAttt < 1:818566/42‑1 (MQ=255)
gATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcatca < 1:487634/70‑1 (MQ=255)
gATTGTTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCtcatca < 1:2032456/70‑1 (MQ=255)
gATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCAg > 1:2126155/1‑71 (MQ=255)
gATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCAg > 1:187345/1‑71 (MQ=255)
attattAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGaa < 1:3097386/59‑1 (MQ=255)
ttattaGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCAGt > 1:3452272/1‑70 (MQ=255)
ttattaGTCTTTGCATGAGCAAGCGAACTGATACATATCTCTTTGTTCTCATTCAGAAAATCtca < 1:3953464/65‑1 (MQ=255)
|
AAAATGTTCAGAAAATAATCCATGGAAAATTGTCCGGAGCACTTACTATTTTAATGGATTATTAGTCTTTGCATGAGCAAGCGAACTGATACATTTCTCTTTGTTCTCATTCAGAAAATCTCATCAGT > minE/2823811‑2823938
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
