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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,641,490:1 |
+G |
23.7% |
coding (113/1425 nt) |
creC → |
sensory histidine kinase in two‑component regulatory system with CreB or PhoB, regulator of the CreBC regulon |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,641,490 | 1 | . | G | 23.7%
| 57.3
/ 43.2
| 38 | coding (113/1425 nt) | creC | sensory histidine kinase in two‑component regulatory system with CreB or PhoB, regulator of the CreBC regulon |
| Reads supporting (aligned to +/- strand): ref base . (13/16); new base G (3/6); total (16/22) |
| Fisher's exact test for biased strand distribution p-value = 7.06e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGG > W3110S.gb/4641423‑4641557
|
gcggtggcAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑g > 1:3014212/1‑69 (MQ=255)
gcAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑gg > 1:2476141/1‑64 (MQ=255)
ccTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGtt < 1:2764283/71‑1 (MQ=255)
cTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTg < 1:702707/71‑1 (MQ=255)
tCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGa > 1:1654089/1‑70 (MQ=255)
cGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGac < 1:3495013/70‑1 (MQ=255)
gTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑gg < 1:96093/52‑1 (MQ=255)
cTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑ggga > 1:3113445/1‑49 (MQ=255)
ggCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGaca > 1:4236610/1‑65 (MQ=255)
aTTTTTGTCAAAGAAGTTAACCCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTGATc < 1:1166116/58‑1 (MQ=255)
aTTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGtt < 1:119610/71‑1 (MQ=255)
tttttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACg < 1:4442759/50‑1 (MQ=255)
ttttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATc < 1:2703494/55‑1 (MQ=255)
ttttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGc > 1:3373216/1‑71 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAc > 1:262731/1‑38 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTGAt > 1:3995661/1‑54 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGa > 1:4109331/1‑41 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAAc > 1:2855445/1‑65 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCt > 1:2405645/1‑71 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCt > 1:2847228/1‑71 (MQ=255)
tttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCt > 1:4344218/1‑71 (MQ=255)
ttGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTGAt > 1:1441167/1‑53 (MQ=255)
aaaGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGa > 1:4317005/1‑50 (MQ=255)
aagaagTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTgg < 1:1535266/66‑1 (MQ=255)
gaagTTAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTGATCGa < 1:3529456/48‑1 (MQ=255)
aagTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTg < 1:526347/71‑1 (MQ=255)
gTTAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTGATCGACACCGCAACGTTGCTgg < 1:1582320/62‑1 (MQ=255)
gTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGgc < 1:3209038/71‑1 (MQ=255)
ttAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCgg < 1:389701/63‑1 (MQ=255)
tAAACCGGGCGTGCGAAGAGCAACGGGAGGGGACGTTGATCGacac > 1:3327565/1‑46 (MQ=255)
aaaCCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGt > 1:973285/1‑52 (MQ=255)
aaaCCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGcgcg > 1:4533478/1‑71 (MQ=255)
aaCCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGAAACCGCAACGTTGCTGGCGGAGCTGGcgcg < 1:1991658/70‑1 (MQ=255)
cGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACCCCGCAACGTTGCTGGCGGAGCTGGCGCGt > 1:1336774/1‑68 (MQ=255)
ggCGTGCGAAGAGCAAC‑GGAGTGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGa < 1:2126260/71‑1 (MQ=255)
gTGCGAAGAGCAACGGGAGGGGACGTTGATCGACACCGCAACGTTGCTgg < 1:3814844/50‑1 (MQ=255)
tGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTg < 1:3415274/71‑1 (MQ=255)
cGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGct < 1:2191440/71‑1 (MQ=255)
gagCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGctctct < 1:777470/71‑1 (MQ=255)
agCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCt < 1:254093/39‑1 (MQ=255)
gCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTg < 1:2661454/70‑1 (MQ=255)
cAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTggg < 1:947520/71‑1 (MQ=255)
cAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTggg > 1:1279666/1‑71 (MQ=255)
|
GCGGTGGCAGCCTGGTTCGTACTGGCCATTTTTGTCAAAGAAGTTAAACCGGGCGTGCGAAGAGCAAC‑GGAGGGGACGTTGATCGACACCGCAACGTTGCTGGCGGAGCTGGCGCGTCCCGATTTGCTCTCTGGG > W3110S.gb/4641423‑4641557
|
| 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
