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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,532,234 |
C→T |
100% |
P164P (CCG→CCA) |
aroC ← |
chorismate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,532,234 | 0 | C | T | 91.1%
| 38.9
/ ‑3.2
| 22 | P164P (CCG→CCA) | aroC | chorismate synthase |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base T (0/20); total (1/21) |
| Fisher's exact test for biased strand distribution p-value = 9.09e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGACCTGCGACCAGTCTTTGATATCCAGCGGAATGTCGCCCATCTGGGTCAGGCAGCCACGGATTTCAATACCAAATTTCTCGGCGAGATATTTT > minE/1532206‑1532300
|
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2528438/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:461837/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:384659/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:3433037/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:3195152/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2996289/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2994602/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2938176/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:277767/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2646980/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:1098693/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2307573/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:1796947/69‑1 (MQ=255)
cGACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:1785016/69‑1 (MQ=255)
gACCTGAGACCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCaa < 1:2470535/68‑1 (MQ=255)
aCCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCAATGCCAAAt < 1:1585249/68‑1 (MQ=255)
aCCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCAATGCCAAAt < 1:1511539/68‑1 (MQ=255)
aCCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCAATGCCAAAt < 1:3226501/68‑1 (MQ=255)
aCCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCAATGCCAAAt < 1:1375292/68‑1 (MQ=255)
aCCAGTCTTTGATTTCCAGTGGAATGTCGCCCATCTGGGTCAGGCAACCGCGAATCTCAATGCCAAAt < 1:1358441/68‑1 (MQ=255)
tGATATCCAGCGGAATGTCGCCCATCTGGGTCAGGCAGCCACGGATTTCAATACCAAATTTCTCg > 1:1286996/1‑65 (MQ=255)
gCGGAATGTCGCCCATCTGGGTCAGGCAGCCACGGATTTCAATACCAAATTTCTCGGCGAGATAtttt < 1:2305508/68‑1 (MQ=255)
|
CGACCTGCGACCAGTCTTTGATATCCAGCGGAATGTCGCCCATCTGGGTCAGGCAGCCACGGATTTCAATACCAAATTTCTCGGCGAGATATTTT > minE/1532206‑1532300
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
