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 F8 I0 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,230,217 |
A→G |
36.0% |
intergenic (+322/‑104) |
ygjK → / → fadH |
predicted glycosyl hydrolase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,230,217 | 0 | A | G | 36.0%
| 43.0
/ 50.2
| 50 | intergenic (+322/‑104) | ygjK/fadH | predicted glycosyl hydrolase/2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| Reads supporting (aligned to +/- strand): ref base A (20/12); new base G (13/5); total (33/17) |
| Fisher's exact test for biased strand distribution p-value = 5.48e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.17e-01 |
CAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGACGGCTAAATTAG > W3110S.gb/3230147‑3230274
|
cAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGaa > 1:358672/1‑71 (MQ=255)
aTTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAGTc > 1:2156360/1‑71 (MQ=255)
ccGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCa > 1:3679501/1‑71 (MQ=255)
ccGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCa > 1:3600122/1‑71 (MQ=255)
ccGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCa > 1:2922643/1‑71 (MQ=255)
aaCCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAAt > 1:1285792/1‑63 (MQ=255)
aaCCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAAt > 1:1510738/1‑63 (MQ=255)
ccTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACaa < 1:1343663/71‑1 (MQ=255)
gATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAAccc > 1:2679363/1‑71 (MQ=255)
gATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAAccc > 1:2311686/1‑71 (MQ=255)
gATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAAccc > 1:3769814/1‑71 (MQ=255)
tAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACaaa > 1:1150334/1‑66 (MQ=255)
cgcgACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATc > 1:126555/1‑51 (MQ=255)
cgcgACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATc > 1:2025715/1‑51 (MQ=255)
cgcgACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATc > 1:1543312/1‑51 (MQ=255)
cgACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTccc > 1:2455361/1‑71 (MQ=255)
cgACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTccc > 1:2541469/1‑71 (MQ=255)
gACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTcccc < 1:3415286/71‑1 (MQ=255)
gACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTcccc < 1:1649220/71‑1 (MQ=255)
aCAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTcccc < 1:361705/70‑1 (MQ=255)
aaGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACt > 1:1504044/1‑64 (MQ=255)
tCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTCcccttttccc < 1:1707603/70‑1 (MQ=255)
gCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACTCcccttttcccttt < 1:75907/71‑1 (MQ=255)
gCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACaaa > 1:177241/1‑48 (MQ=255)
gCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACaaa > 1:3703571/1‑48 (MQ=255)
cGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTcc < 1:2149599/71‑1 (MQ=255)
cGGCGTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTcc < 1:2670407/71‑1 (MQ=255)
cGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTtctc > 1:865034/1‑70 (MQ=255)
cGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGc < 1:3266604/71‑1 (MQ=255)
gTTATCACCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACTCcccttttccctt > 1:3669544/1‑61 (MQ=255)
gTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCg < 1:3660511/44‑1 (MQ=255)
aTCACCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGACg > 1:2003816/1‑71 (MQ=255)
aTCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGAc > 1:3100477/1‑70 (MQ=255)
aCCGGGCGTATTCTTTTTGAGTCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGACGGCt < 1:198460/71‑1 (MQ=255)
tATTCTTTTTGAGTCCCATCACAAACCCCGCACTcc < 1:842733/36‑1 (MQ=255)
tATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGc < 1:2709083/56‑1 (MQ=255)
tATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGc < 1:3670858/56‑1 (MQ=255)
tATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGACGGCTa < 1:856140/64‑1 (MQ=255)
ttCTTTTTGAGTCCCATCACAAACCCCGCACTcccc > 1:3410139/1‑36 (MQ=255)
ttCTTTTTGAGTCCCATCACAAACCCCGCACTcccc > 1:3706909/1‑36 (MQ=255)
ttCTTTTTGAGTCCCATCACAAACCCCGCACTcccc > 1:695313/1‑36 (MQ=255)
ttCTTTTTGAGTCCCATCACAAACCCCGCACTccc > 1:2392806/1‑35 (MQ=255)
ttCTTTTTGAATCCCATCACAAACCCCGCCCTCcccttttcccttt > 1:3811347/1‑46 (MQ=255)
ttCTTTTTGAATCCCATCACAAACCCCGCACTCcccttttcccttt > 1:2839759/1‑46 (MQ=255)
ttCTTTTTGAATCCCATCACAAACCCCGCACTCcccttttcccttt > 1:2053496/1‑46 (MQ=255)
ttCTTTTTGAATCCCATCACAAACCCCGCACTCcccttttccc < 1:1735840/43‑1 (MQ=255)
cTTTTTGAGTCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCgg > 1:2956347/1‑51 (MQ=255)
cTTTTTGAGTCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCg > 1:1578786/1‑50 (MQ=255)
cTTTTTGAATCCCATCACAAACCCCGCACTCcccttttccctt > 1:1441420/1‑43 (MQ=255)
cTTTTTGAATCCCATCACAAACCCCGCACTCcccttttccctt > 1:1464299/1‑43 (MQ=255)
tttttGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGACGGCTAAATTAg < 1:3479397/65‑1 (MQ=255)
|
CAATTCCGTAACCTGGATAAAACGCGACAAGCGTCGCATCCGGCGTTATCACCGGGCGTATTCTTTTTGAATCCCATCACAAACCCCGCACTCCCCTTTTCCCTTTTCTCCGGCGACGGCTAAATTAG > W3110S.gb/3230147‑3230274
|
| 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
