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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
349,140 |
C→T |
36.4% |
intergenic (+344/‑96) |
prpB → / → prpC |
2‑methylisocitrate lyase/2‑methylcitrate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 349,140 | 0 | C | T | 36.4%
| 43.9
/ 43.0
| 44 | intergenic (+344/‑96) | prpB/prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| Reads supporting (aligned to +/- strand): ref base C (11/17); new base T (5/11); total (16/28) |
| Fisher's exact test for biased strand distribution p-value = 7.48e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCG > W3110S.gb/349084‑349203
|
aTAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:126084/71‑1 (MQ=34)
tAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:498912/70‑1 (MQ=35)
tAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:285113/70‑1 (MQ=35)
aGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactg < 1:1333448/69‑1 (MQ=35)
gCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactgaac > 1:3612113/1‑71 (MQ=34)
gCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaactgaa > 1:4505997/1‑70 (MQ=35)
tCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTc > 1:4637727/1‑71 (MQ=21)
tCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGaactgaactg < 1:1321276/65‑1 (MQ=35)
cGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGtgaactgaa > 1:1115770/1‑60 (MQ=255)
cGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGtgaactgaa > 1:3392178/1‑60 (MQ=255)
ccgccGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGAt < 1:1117972/67‑1 (MQ=25)
aaCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:501144/71‑1 (MQ=21)
aaCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:5087049/71‑1 (MQ=21)
aaCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:865150/71‑1 (MQ=34)
aCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:2515548/70‑1 (MQ=25)
cGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGAc < 1:2908354/71‑1 (MQ=21)
gATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACg > 1:2260626/1‑71 (MQ=34)
gATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACg < 1:4095089/71‑1 (MQ=34)
aTGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACg > 1:907201/1‑70 (MQ=35)
aTGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGc < 1:4656341/71‑1 (MQ=34)
gCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCa > 1:3378091/1‑70 (MQ=35)
aTGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCg < 1:2228245/70‑1 (MQ=35)
tGCGCCGCTGACGCGACTTATCAGGCTTACGGGGTGaactgaactg < 1:3539094/46‑1 (MQ=255)
tGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaac > 1:4982066/1‑39 (MQ=40)
tGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaac > 1:2064434/1‑39 (MQ=40)
tGCGCCGCTGACGCGACTTATCAGGCCTACGGGGtgaac > 1:2995441/1‑39 (MQ=40)
cgccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCg > 1:3154348/1‑70 (MQ=35)
gccgcTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCa < 1:3620513/71‑1 (MQ=21)
gccgcTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACTCATAGCg < 1:4520924/66‑1 (MQ=25)
ccgcTGACGCGACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCa < 1:2788209/70‑1 (MQ=25)
gACGCGAATTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGa > 1:4984638/1‑70 (MQ=25)
gcgACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGacaa > 1:4926644/1‑70 (MQ=25)
gcgACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGacaac < 1:1508881/71‑1 (MQ=34)
gACTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGAcaacaa < 1:335603/71‑1 (MQ=255)
aCTTATCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGacaaca < 1:4654992/69‑1 (MQ=255)
aTCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc > 1:4500594/1‑70 (MQ=255)
aTCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc < 1:4962243/70‑1 (MQ=255)
aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc > 1:1705451/1‑70 (MQ=255)
aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc < 1:4043047/70‑1 (MQ=255)
aTCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAAtctc < 1:219014/70‑1 (MQ=255)
tCAGGCTTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCg < 1:1848516/70‑1 (MQ=255)
tCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:966645/38‑1 (MQ=40)
tCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCg < 1:798706/70‑1 (MQ=255)
cAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATaa < 1:4449931/37‑1 (MQ=40)
|
ATAGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCTACGGGGTGAACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCCGACAACAATCTCG > W3110S.gb/349084‑349203
|
| 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
