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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,584,576 |
G→A |
8.9% |
P21S (CCA→TCA) |
hemN ← |
coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,584,576 | 0 | G | A | 8.9%
| 135.8
/ 3.8
| 45 | P21S (CCA→TCA) | hemN | coproporphyrinogen III oxidase, SAM and NAD(P)H dependent, oxygen‑independent |
| Reads supporting (aligned to +/- strand): ref base G (19/22); new base A (2/2); total (21/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01 |
TAAAAACGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAGACATGCTCACTCCT > W3110S.gb/3584511‑3584646
|
tAAAAACGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCgg < 1:1044158/71‑1 (MQ=255)
tAAAAACGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCg > 1:2744098/1‑70 (MQ=255)
tAAAAACGCCTGTTAGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCg > 1:518516/1‑70 (MQ=255)
aaaaCGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGaa > 1:1166437/1‑71 (MQ=255)
aCGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGaa < 1:2931846/68‑1 (MQ=255)
gTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTatat > 1:1224835/1‑71 (MQ=255)
ttCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTatat < 1:1703351/70‑1 (MQ=255)
tCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGc > 1:192380/1‑54 (MQ=255)
tCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATAttt > 1:4363751/1‑71 (MQ=255)
gCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCt < 1:1286046/71‑1 (MQ=255)
cGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTgg < 1:1046015/49‑1 (MQ=255)
aaGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGAt > 1:2859910/1‑71 (MQ=255)
aaGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGAt > 1:2501867/1‑71 (MQ=255)
aaGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGACCCGGAATAGTTATATTTCTGGAt < 1:1238583/71‑1 (MQ=255)
gTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGACCCGGAATAGTTATATTTCTGGATCa < 1:729705/71‑1 (MQ=255)
tctGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGACCCGGAATa > 1:3509103/1‑50 (MQ=255)
ctGAAAACTCCAGGGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGc < 1:2228135/70‑1 (MQ=255)
ctGAAAACTCCAGCGCGGTCGGGTACGATGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAgg < 1:201848/68‑1 (MQ=255)
gAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGccc > 1:4052320/1‑41 (MQ=255)
gAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCgg < 1:1890699/43‑1 (MQ=255)
aaaaCTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGc > 1:3927397/1‑67 (MQ=255)
aaaaCTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAg < 1:1226142/70‑1 (MQ=255)
aaaaCTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGa < 1:4581644/71‑1 (MQ=255)
aaaCTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATAATTCTGGATCAGGGc > 1:571419/1‑66 (MQ=255)
aaCTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATc > 1:2379205/1‑71 (MQ=255)
aCTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATAttt < 1:4400610/52‑1 (MQ=255)
cTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCt > 1:1031319/1‑53 (MQ=255)
cTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATccc < 1:4226242/71‑1 (MQ=255)
tCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTc < 1:3423097/51‑1 (MQ=255)
cAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATc > 1:1782989/1‑66 (MQ=255)
gcgcGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCg < 1:3732152/71‑1 (MQ=255)
cgcgGTCGGGAACGAGGTGTATCGTGGCCCGGAATa < 1:3354542/36‑1 (MQ=255)
tCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTc < 1:1803597/64‑1 (MQ=255)
gggTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTg > 1:873951/1‑71 (MQ=255)
gggTACGAGGTGTATCGTGACCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTg > 1:1148558/1‑71 (MQ=255)
ggTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGt < 1:21787/71‑1 (MQ=255)
tACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTa > 1:553112/1‑70 (MQ=255)
cGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAg < 1:3914337/71‑1 (MQ=255)
cGAGGTGTATCGTGGCCAGGAATAGTTATATTTCTGGATGAGGGCCAGATCCCAGTCGATTTGCTGTa > 1:2996466/1‑68 (MQ=255)
ggTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAGACa > 1:1549258/1‑71 (MQ=255)
ggTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCAAGTCGATTTGCTGTACAGACa < 1:1755149/71‑1 (MQ=255)
tgtATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGACAGATCCCAGTCGATTTGCTGTACAGACATg < 1:4345649/71‑1 (MQ=255)
tCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGAtt > 1:3976422/1‑52 (MQ=255)
tCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTg < 1:208606/57‑1 (MQ=255)
gTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAGACATg < 1:1043173/65‑1 (MQ=255)
gTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAGACATGCTCAc < 1:2214028/70‑1 (MQ=255)
gCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAGACATGCTCACTCCt < 1:3966139/71‑1 (MQ=255)
|
TAAAAACGCCTGTTCGCCGAAGTCTTCTGAAAACTCCAGCGCGGTCGGGTACGAGGTGTATCGTGGCCCGGAATAGTTATATTTCTGGATCAGGGCCAGATCCCAGTCGATTTGCTGTACAGACATGCTCACTCCT > W3110S.gb/3584511‑3584646
|
| 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
