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 |
2,560,276 |
C→T |
45.4% |
intergenic (‑16/+182) |
yibK ← / ← lldD |
predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,560,276 | 0 | C | T | 45.4%
| 14.5
/ 52.1
| 44 | intergenic (‑16/+182) | yibK/lldD | predicted rRNA methylase/L‑lactate dehydrogenase, FMN‑linked |
| Reads supporting (aligned to +/- strand): ref base C (12/12); new base T (8/12); total (20/24) |
| Fisher's exact test for biased strand distribution p-value = 5.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGATGTTGCCAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCTCACCCCGGCCCTCTCCCCGG > minE/2560206‑2560343
|
tgatgTTGCCAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGc < 1:669263/71‑1 (MQ=255)
atgTTGCCAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTgg > 1:3031743/1‑71 (MQ=255)
tgTTGCCAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCggg < 1:3301631/71‑1 (MQ=255)
ttGCCAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGc < 1:3292459/66‑1 (MQ=255)
ccAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAg < 1:966814/71‑1 (MQ=255)
ccAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAg < 1:3560883/71‑1 (MQ=255)
ccAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCa < 1:2441324/70‑1 (MQ=255)
tATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAg < 1:958847/67‑1 (MQ=255)
aTTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAg > 1:1881939/1‑71 (MQ=255)
gCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGaa < 1:3973549/71‑1 (MQ=255)
ggAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGaaaa < 1:1040052/71‑1 (MQ=255)
aaTTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGa > 1:3344383/1‑59 (MQ=255)
aaTTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGAt < 1:3477656/60‑1 (MQ=255)
aaTTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGaaaa > 1:1773301/1‑69 (MQ=255)
tttCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGc < 1:2830053/47‑1 (MQ=255)
gTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGATa < 1:2513498/53‑1 (MQ=255)
gTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGc < 1:770627/70‑1 (MQ=255)
ttCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGc < 1:1781391/40‑1 (MQ=255)
tCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGa > 1:730290/1‑49 (MQ=255)
tCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGa > 1:873616/1‑49 (MQ=255)
cGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGa > 1:1073515/1‑48 (MQ=255)
gTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGa > 1:1651054/1‑47 (MQ=255)
gTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGa > 1:3557506/1‑47 (MQ=255)
gTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGaa < 1:1117003/55‑1 (MQ=255)
tAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCg < 1:1567067/71‑1 (MQ=255)
tAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAg < 1:940850/44‑1 (MQ=255)
tAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCg < 1:3031544/71‑1 (MQ=255)
aaGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGc > 1:3841703/1‑71 (MQ=255)
aGTACGATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAAt > 1:208521/1‑54 (MQ=255)
cGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGGAAATTGGTGAGCAg > 1:690812/1‑60 (MQ=255)
cGATGTTTAGCATACTGCCCCCTTACTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCttt < 1:2506652/70‑1 (MQ=255)
gATGTTTAGCATACTGCCCCCTTAGTGTGGGGGCAGGATAg < 1:1386473/41‑1 (MQ=255)
tGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAg > 1:3362725/1‑57 (MQ=255)
tttAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCt < 1:76512/71‑1 (MQ=255)
gCATACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTg < 1:2785384/43‑1 (MQ=255)
gCATACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCTCAc < 1:2765189/70‑1 (MQ=255)
tACTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCt > 1:3894285/1‑56 (MQ=255)
cTGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCTCACCCCgg < 1:405848/70‑1 (MQ=255)
tGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCa > 1:1957044/1‑44 (MQ=255)
tGCCCCCTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCa > 1:1962024/1‑44 (MQ=255)
ccccTTAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCTCACCCCGGcc < 1:3439566/68‑1 (MQ=255)
cccTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCtt < 1:2401484/50‑1 (MQ=255)
ccTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTc < 1:1876351/52‑1 (MQ=255)
cTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGc < 1:3280271/37‑1 (MQ=255)
tAGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCtt > 1:1920684/1‑46 (MQ=255)
aGTGTGGGGGCAGGATAGCAGAAAATTGGTGAGCa > 1:1310660/1‑35 (MQ=255)
aGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCa > 1:4118928/1‑35 (MQ=255)
aGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCa > 1:3800670/1‑35 (MQ=255)
gtgtGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCTCACCCCGGCCCTCTCCCCgg < 1:563932/71‑1 (MQ=255)
|
TGATGTTGCCAGTATTTGGCGGAATTTCTGGTTCGTAAAGTACGATGTTTAGCATACTGCCCCCTTAGTGCGGGGGCAGGATAGCAGAAAATTGGTGAGCAGTGCGGCCTTTTCCCCTCACCCCGGCCCTCTCCCCGG > minE/2560206‑2560343
|
| 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
