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 |
2,315,568 |
A→G |
100% |
G172G (GGT→GGC) |
ompC ← |
outer membrane porin protein C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,315,568 | 0 | A | G | 87.0%
| 60.1
/ 2.2
| 23 | G172G (GGT→GGC) | ompC | outer membrane porin protein C |
| Reads supporting (aligned to +/- strand): ref base A (3/0); new base G (5/15); total (8/15) |
| Fisher's exact test for biased strand distribution p-value = 3.16e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTC > W3110S.gb/2315504‑2315600
|
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:86131/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:1128674/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:7610/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:618094/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:1962564/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:54500/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:266400/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:332952/71‑1 (MQ=255)
gTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTgg < 1:424591/71‑1 (MQ=255)
gCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGTGTTGCCGTTTTTGCCCTgg < 1:1782127/69‑1 (MQ=255)
aCGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGaa > 1:1385515/1‑71 (MQ=255)
aCGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGaa > 1:58169/1‑71 (MQ=255)
aCGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGa > 1:256391/1‑70 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGcc > 1:1073512/1‑71 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGcc > 1:643532/1‑71 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGcc > 1:264406/1‑71 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGcc > 1:1440929/1‑71 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGcc > 1:1059493/1‑71 (MQ=255)
ccACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTc < 1:43144/71‑1 (MQ=255)
ccACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTc < 1:151387/71‑1 (MQ=255)
ccACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTc < 1:1211121/71‑1 (MQ=255)
ccACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTc < 1:968005/71‑1 (MQ=255)
cACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTc < 1:1704342/70‑1 (MQ=255)
|
GTGCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTC > W3110S.gb/2315504‑2315600
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
