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 |
|
A142 F1 I1 R1
|
21 |
42.6 |
2691336 |
96.3% |
2591756 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,893,551 |
+G |
intergenic (+6/‑50) |
kup → / → insJ‑5 |
potassium transporter/IS150 hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,893,550 | 1 | . | G | 95.3%
| 155.9
/ 0.4
| 43 | intergenic (+5/‑51) | kup/insJ‑5 | potassium transporter/IS150 hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base G (24/17); total (26/17) |
| Fisher's exact test for biased strand distribution p-value = 5.11e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
TGCGTGCACCAGATCAATTTGAAATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCA‑GACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCAAAATACC > REL606/3893475‑3893619
|
tGCGTGCACCAGATCGATTTGAAATCCCGCCAATCAGGGTTATCGAACTGGGTACTCAGGTNGAAATCTAACG‑CCa > 1:1153291/1‑76 (MQ=255)
tGCGTGCACCAGATCAATTTGAAATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCa > 1:863095/1‑76 (MQ=255)
gCGTGCACCAGATCAATTTGAAATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCA‑g < 1:857365/76‑1 (MQ=255)
gTGCACCAGATCAATTTGACATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCA‑gga > 2:749953/1‑74 (MQ=255)
tGCACCAGATCAATTTGAAATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAATN‑CCA‑ggac < 2:1084454/76‑4 (MQ=255)
aaTTTGAAATCCCGCCACACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAGCG‑CCAGGACTGTACTGCAcc > 1:1325205/1‑76 (MQ=255)
aaaTCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCAtttt > 2:93334/1‑76 (MQ=255)
cccGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTttgttg < 1:150977/76‑1 (MQ=255)
cGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGa < 1:882792/76‑1 (MQ=255)
gCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGAc > 1:337498/1‑76 (MQ=255)
gCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGCACTGCACCCATTTTGTTGGAc > 1:421594/1‑76 (MQ=39)
ccAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACg < 1:693866/76‑1 (MQ=255)
cAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGa > 1:671915/1‑76 (MQ=255)
aaaCAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGAt > 2:631543/1‑76 (MQ=255)
aGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAAGGCCCG‑GACTGTACTGCACTCATTTTGTTGGACGATGaaa > 2:1059051/1‑76 (MQ=25)
aGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGaaa > 1:740134/1‑76 (MQ=255)
ggTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATg < 2:244661/76‑1 (MQ=255)
ttATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGa < 2:301496/76‑1 (MQ=255)
ttATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGa > 1:824522/1‑76 (MQ=255)
ttATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCA‑GACTGTACTGCACCCATTTTGTTGGACGATGAAATGGaa > 2:135209/1‑76 (MQ=255)
tATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGaa > 2:502182/1‑76 (MQ=255)
aTCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAAt < 1:1222774/76‑1 (MQ=255)
tCGAATGGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGCTGAAATGGAATa < 2:56562/76‑1 (MQ=21)
tCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATa < 1:1109948/76‑1 (MQ=255)
tCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATa < 2:1220117/76‑1 (MQ=255)
tCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATa < 2:1220123/76‑1 (MQ=255)
tCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATa < 2:384021/76‑1 (MQ=255)
cGAACTGGGTACTCATGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAg > 2:719792/1‑76 (MQ=21)
cGAACTGGGTACTCACGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAg > 2:719776/1‑76 (MQ=21)
gAACTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGc > 2:1044491/1‑76 (MQ=255)
aCTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGccc > 2:749273/1‑76 (MQ=255)
cTGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGcccc > 2:777881/1‑76 (MQ=255)
tGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCt > 1:140537/1‑76 (MQ=255)
tGGGTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCt < 2:1174168/76‑1 (MQ=255)
ggTACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTaa > 1:864774/1‑76 (MQ=255)
tACTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAata < 2:741055/76‑1 (MQ=255)
aCTCAGGTCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAatat > 2:245831/1‑76 (MQ=255)
tCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAg < 2:159366/76‑1 (MQ=255)
tCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAg > 2:841337/1‑76 (MQ=255)
tCGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAg > 1:944495/1‑76 (MQ=255)
cGAAATCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGc > 2:32832/1‑76 (MQ=255)
naaTCTAACG‑CCAGGACTGTACTGCACCCATTTTCTTNGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCa > 1:1308885/2‑76 (MQ=14)
aaaTCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCa < 2:415223/76‑1 (MQ=255)
aaaTCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCa < 1:380245/76‑1 (MQ=255)
aaaTCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCa > 2:1007810/1‑76 (MQ=255)
aaaTCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCa > 2:781267/1‑76 (MQ=255)
tCTAACG‑CCAGGACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCaaaa > 1:439395/1‑76 (MQ=255)
aCG‑CCAGGACTGTACTGTAGCCTTTTTGTTGGACGATGAAATGGAATAGCCGCTAGTATGTCAAAGCCAAAATAcc < 1:64603/76‑1 (MQ=11)
|
TGCGTGCACCAGATCAATTTGAAATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTCGAAATCTAACG‑CCA‑GACTGTACTGCACCCATTTTGTTGGACGATGAAATGGAATAGCCCCTAATATGTCAAAGCCAAAATACC > REL606/3893475‑3893619
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
