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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,832,029 |
A→G |
46.7% |
intergenic (‑152/‑290) |
kdtA ← / → rfaQ |
3‑deoxy‑D‑manno‑octulosonic‑acid transferase/lipopolysaccharide core biosynthesis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,832,029 | 0 | A | G | 46.7%
| ‑0.4
/ 41.0
| 30 | intergenic (‑152/‑290) | kdtA/rfaQ | 3‑deoxy‑D‑manno‑octulosonic‑acid transferase/lipopolysaccharide core biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base A (4/12); new base G (4/10); total (8/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAATAGCTTCAGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCATTTTCAAATCTACATAGGCCGTACTGACATTATCGA > W3110S.gb/3831960‑3832077
|
aaaTAGCTTCAGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGa < 1:1634532/70‑1 (MQ=255)
aaaTAGCTTCAGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGa < 1:260398/70‑1 (MQ=255)
aaaTAGCTTCAGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGa < 1:1883475/70‑1 (MQ=255)
aaaTAGCTTCAGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGa < 1:1249146/70‑1 (MQ=255)
aGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGccc < 1:1338898/70‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:134335/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:258931/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:629123/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:1548379/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:1595089/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:1883770/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:409589/71‑1 (MQ=255)
gTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:1821311/71‑1 (MQ=255)
tGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCAttt > 1:1740989/1‑71 (MQ=255)
tGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCAttt > 1:375176/1‑71 (MQ=255)
tGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCAtt > 1:1362543/1‑70 (MQ=255)
cTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCa < 1:101934/64‑1 (MQ=255)
cTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCATTTTCAAATCTa > 1:330786/1‑71 (MQ=255)
ccGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTa < 1:1225557/68‑1 (MQ=255)
ccGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTa < 1:692480/68‑1 (MQ=255)
ccGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa < 1:520588/70‑1 (MQ=255)
ccGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa < 1:1848162/70‑1 (MQ=255)
ccGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa < 1:838250/70‑1 (MQ=255)
ccGCTACATCTTCATTTTTTTTGTATTCTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa < 1:383141/70‑1 (MQ=255)
ccGCTACATCCTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTa < 1:1784831/68‑1 (MQ=255)
gCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa > 1:178829/1‑68 (MQ=255)
gCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa > 1:1759245/1‑68 (MQ=255)
gCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa > 1:1394500/1‑68 (MQ=255)
gCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACa > 1:645036/1‑68 (MQ=255)
cATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACATAGGc < 1:129623/69‑1 (MQ=255)
cATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACATAGGc < 1:891651/69‑1 (MQ=255)
cATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGGAACTCGGCCCCATTTTCAAATCTACATAGGc < 1:96629/69‑1 (MQ=255)
gTATTTTTATGCGATTCATTGAAACTCGGCCCCATTTTCAAATCTACATAGGCCGTACTGACATTATCGa < 1:1968555/70‑1 (MQ=255)
gTATTTTTATGCGATTCATTGAAACTCGGCCCCATTTTCAAATCTACATAGGCCGTACTGACATTATCGa < 1:1364575/70‑1 (MQ=255)
|
AAATAGCTTCAGTTTGGTCTGATCTGCCGCTACATCTTCATTTTTTTTGTATTTTTATGCGATTCATTGAAACTCGGCCCCATTTTCAAATCTACATAGGCCGTACTGACATTATCGA > W3110S.gb/3831960‑3832077
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
