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 |
|
A1 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,354,061 |
C→T |
15.9% |
G218G (GGG→GGA) |
dcuR ← |
DNA‑binding response regulator in two‑component regulatory system with DcuS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,354,061 | 0 | C | T | 15.9%
| 141.6
/ 18.1
| 57 | G218G (GGG→GGA) | dcuR | DNA‑binding response regulator in two‑component regulatory system with DcuS |
| Reads supporting (aligned to +/- strand): ref base C (17/30); new base T (5/4); total (22/35) |
| Fisher's exact test for biased strand distribution p-value = 2.94e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01 |
CCGTTATTGGCAATATTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAGGTATTTACG > W3110S.gb/4353992‑4354129
|
ccGTTATTGGCAATATTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGcc > 1:2771826/1‑71 (MQ=255)
ccGTTATTGGCAATATTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGcc > 1:2421827/1‑71 (MQ=255)
aTTGGCAATATTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGt < 1:1652211/70‑1 (MQ=255)
atatTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCAt < 1:238351/71‑1 (MQ=255)
atatTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCAt < 1:2503277/71‑1 (MQ=255)
gTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATg < 1:761707/70‑1 (MQ=255)
gTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATg < 1:1558020/70‑1 (MQ=255)
tttCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGa < 1:289423/71‑1 (MQ=255)
gtagtgagtagtgTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTg < 1:839922/71‑1 (MQ=255)
gtgagtagtgTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGt < 1:1905108/70‑1 (MQ=255)
tgagtagtgTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCAt < 1:369398/56‑1 (MQ=255)
agtagtgTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCAGTGACGCAATaa > 1:738251/1‑56 (MQ=255)
agtgTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAAc > 1:2103482/1‑68 (MQ=255)
gtgtTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGa < 1:2395041/71‑1 (MQ=255)
gtgtTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGa < 1:804038/71‑1 (MQ=255)
gtgtGCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCAt < 1:885228/50‑1 (MQ=255)
tgtTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATa < 1:676722/50‑1 (MQ=255)
tgtTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATa < 1:2575132/50‑1 (MQ=255)
tgtTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATa < 1:2102348/50‑1 (MQ=255)
tgtTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGAt > 1:451261/1‑71 (MQ=255)
ttCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGt < 1:169341/39‑1 (MQ=255)
ttCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGAtgt > 1:80980/1‑71 (MQ=255)
ttCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGAtgt > 1:293699/1‑71 (MQ=255)
ttCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGAtgt > 1:1086643/1‑71 (MQ=255)
ttCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGAtgt > 1:1724819/1‑71 (MQ=255)
cTGCCTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTgg > 1:781246/1‑71 (MQ=255)
cTGCCTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTgg > 1:1249541/1‑71 (MQ=255)
cTGCCTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTgg > 1:2524289/1‑71 (MQ=255)
cTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTgg > 1:342312/1‑71 (MQ=255)
gCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCAt < 1:357738/43‑1 (MQ=255)
ccTGAATACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTTGCa < 1:1889358/70‑1 (MQ=255)
aaTACGGTAACGGTAAACTGGACGTCCCGTGACGCCATAATGGa > 1:803910/1‑44 (MQ=255)
aaTACGGTAACGGTAAACTGGACGCCCCGTGACTCCATAATGGATACTGGTGAACAAGATGTGGc < 1:1242404/65‑1 (MQ=255)
aaTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGGAGTTGa < 1:6270/71‑1 (MQ=255)
aaTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGa > 1:2557207/1‑71 (MQ=255)
aaTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGa > 1:792262/1‑71 (MQ=255)
aaTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTCGCAGTTGa > 1:2609167/1‑71 (MQ=255)
aaTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGAATACTGGTGAACAAGATGTGGCAGtt < 1:774122/69‑1 (MQ=255)
aTACGGTAACGGTAAACTGGACGCCCCGTGACGCCAt < 1:2041018/37‑1 (MQ=255)
aTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGa < 1:1659678/43‑1 (MQ=255)
aTACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACaa < 1:47560/56‑1 (MQ=255)
cggtaacggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGAt > 1:906578/1‑56 (MQ=255)
cggtaacggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGAccag > 1:967804/1‑71 (MQ=255)
ggtaacggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGAccagc < 1:1146722/71‑1 (MQ=255)
gtaacggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACaa < 1:119863/51‑1 (MQ=255)
gtaacggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGAc > 1:2253671/1‑66 (MQ=255)
gtaacggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGAc > 1:2081345/1‑66 (MQ=255)
gtaacggtaaACTGGACG‑CCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGAccagcca < 1:681939/71‑1 (MQ=255)
ggtaaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGAt < 1:103642/70‑1 (MQ=255)
gtaaACTGGACGTCCAGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGAt > 1:1020523/1‑69 (MQ=255)
taaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATg < 1:221554/69‑1 (MQ=255)
taaACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAg < 1:1452415/71‑1 (MQ=255)
aaCTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGAcca > 1:1918060/1‑59 (MQ=255)
aaCTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAgg < 1:683924/70‑1 (MQ=255)
aaCTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAgg < 1:687291/70‑1 (MQ=255)
aaCTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAgg < 1:137140/70‑1 (MQ=255)
aaCTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAgg < 1:1229285/70‑1 (MQ=255)
aaCTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAGGt < 1:449435/71‑1 (MQ=255)
cGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAGGTATTTACg > 1:534273/1‑71 (MQ=255)
|
CCGTTATTGGCAATATTGTTTCAGTAGTGAGTAGTGTTCTGCCTGAATACGGTAACGGTAAACTGGACGCCCCGTGACGCCATAATGGATACTGGTGAACAAGATGTGGCAGTTGACCAGCCAGATGAGGTATTTACG > W3110S.gb/4353992‑4354129
|
| 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
