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 |
920,527 |
G→A |
100% |
T24T (ACC→ACT) |
mpaA ← |
murein peptide amidase A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 920,527 | 0 | G | A | 77.4%
| 23.6
/ 2.7
| 22 | T24T (ACC→ACT) | mpaA | murein peptide amidase A |
| Reads supporting (aligned to +/- strand): ref base G (2/3); new base A (0/17); total (2/20) |
| Fisher's exact test for biased strand distribution p-value = 4.33e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AACGTCCGTAATGTTCTGTTCCGGGCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAG > minE/920472‑920567
|
aaCGTCCGTAATGTTCTGTTCCGGGCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTAc < 1:1141508/61‑1 (MQ=255)
aaTGTTCTGTTCCGGGCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTACGGTCATGATCGTCTCTg > 1:2716793/1‑69 (MQ=255)
ccGGGCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTACGGTCATGATCGTCTCTGGTTCAGGAAg > 1:1611318/1‑68 (MQ=255)
ccGGGCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTACGGTCATGATCGTCTCTGGTTCAGGAAg < 1:1771384/68‑1 (MQ=255)
ggCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTAt < 1:3358567/68‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:197298/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:702227/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:64702/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:505566/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:3351141/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:3056396/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:2518584/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:2357090/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1956239/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1952228/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1875204/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1567287/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1535876/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1506765/67‑1 (MQ=255)
aaTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1156652/67‑1 (MQ=255)
aTGCGCCGCGTTCGGCGCGTGGGCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:1337319/66‑1 (MQ=255)
gggCGAGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAg < 1:2580578/46‑1 (MQ=255)
|
AACGTCCGTAATGTTCTGTTCCGGGCGGAAATGCGCCGCGTTCGGCGCGTGGGCGGGTTACGGTCATGATCGTCTCTGGTTCAGGAAGTATTACAG > minE/920472‑920567
|
| 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
