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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,441,897 |
C→T |
78.2% |
L462L (TTG→TTA) |
ilvA ← |
threonine deaminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,441,897 | 0 | C | T | 78.2%
| 109.3
/ 29.5
| 55 | L462L (TTG→TTA) | ilvA | threonine deaminase |
| Reads supporting (aligned to +/- strand): ref base C (2/10); new base T (18/25); total (20/35) |
| Fisher's exact test for biased strand distribution p-value = 1.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 |
GGTCGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGG > minE/2441833‑2441962
|
ggTGGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGa > 1:1869585/1‑70 (MQ=255)
gTCGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGaaa > 1:1903305/1‑71 (MQ=255)
gTCGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGaa < 1:1917782/70‑1 (MQ=255)
tCGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAAt < 1:1934302/71‑1 (MQ=255)
tCGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAAt < 1:1929332/71‑1 (MQ=255)
aaGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTcc < 1:2670462/71‑1 (MQ=255)
aaCGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAgtacgt < 1:404469/71‑1 (MQ=255)
aCGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAgtacgt < 1:1057280/70‑1 (MQ=255)
gccgccAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTAcc < 1:300068/71‑1 (MQ=255)
gccgccAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTAcc < 1:4235615/71‑1 (MQ=255)
cgccAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTAcc < 1:370886/69‑1 (MQ=255)
ccAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGc > 1:2513077/1‑71 (MQ=255)
aGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCgt > 1:2048199/1‑71 (MQ=255)
aGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCgt < 1:161890/71‑1 (MQ=255)
aGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCgt < 1:1260275/71‑1 (MQ=255)
aCGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGtt > 1:333531/1‑71 (MQ=255)
aCGCGCCCGTACTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCgt > 1:2462803/1‑68 (MQ=255)
cgcgCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGaaa > 1:1701559/1‑45 (MQ=255)
cgcgCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGtt > 1:807986/1‑70 (MQ=255)
cgcCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAg < 1:2209362/71‑1 (MQ=255)
ccGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTc < 1:4222150/45‑1 (MQ=255)
ccGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTc < 1:493138/45‑1 (MQ=255)
ccGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTc < 1:713973/45‑1 (MQ=255)
ccGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTc < 1:3327234/45‑1 (MQ=255)
ccGTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTc < 1:886675/45‑1 (MQ=255)
gTAGTCGGTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAgc < 1:3796825/71‑1 (MQ=255)
tAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGaa < 1:2677217/36‑1 (MQ=255)
tAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGaa < 1:1877249/36‑1 (MQ=255)
gTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGtt < 1:3461528/60‑1 (MQ=255)
ggTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAg > 1:4147296/1‑60 (MQ=255)
ggTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCgcag > 1:1576058/1‑69 (MQ=255)
gTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAgtacgta < 1:3280298/45‑1 (MQ=255)
gTGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAgtacgta < 1:156420/45‑1 (MQ=255)
tGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCagcagc < 1:832219/71‑1 (MQ=255)
tGCCATGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCagcagc < 1:3672708/71‑1 (MQ=255)
aTGGCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGa > 1:3465742/1‑53 (MQ=255)
gCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCg > 1:4031285/1‑71 (MQ=255)
gCTGCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCg > 1:2998846/1‑71 (MQ=255)
gCGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGt > 1:216803/1‑70 (MQ=255)
cGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGt < 1:3496862/69‑1 (MQ=255)
cGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGt < 1:1506218/69‑1 (MQ=255)
cGATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGt < 1:1851478/69‑1 (MQ=255)
gATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGcagcag > 1:1777840/1‑58 (MQ=255)
gATAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGcagcag > 1:1097424/1‑58 (MQ=255)
tAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCgtg < 1:1819821/39‑1 (MQ=255)
tAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCgtg < 1:4184470/39‑1 (MQ=255)
tAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCgtg < 1:3429516/39‑1 (MQ=255)
tAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCgtg < 1:2238284/39‑1 (MQ=255)
tAGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCgtg < 1:2601602/39‑1 (MQ=255)
aGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTcc > 1:1967094/1‑71 (MQ=255)
aGTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTcc > 1:2767352/1‑71 (MQ=255)
gTGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTcc < 1:4041696/70‑1 (MQ=255)
tGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCgg > 1:3841163/1‑71 (MQ=255)
tGGAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCgg > 1:1219081/1‑71 (MQ=255)
gAATAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCgca < 1:3353934/47‑1 (MQ=255)
|
GGTCGCCAAGTTCGAACGCCGCCAGTACGCGCCCGTAGTCGGTGCCATGGCTGCGATAGTGGAACAAAGAAATGTTCCAGTACGTACCCAGCGTGTTGAGGAAGCGCAGCAGCGCGCCCGGTGATTCCGG > minE/2441833‑2441962
|
| 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
