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 |
1,522,714 |
T→A |
100% |
R130R (CGA→CGT) |
pdxB ← |
erythronate‑4‑phosphate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,522,714 | 0 | T | A | 86.1%
| 70.4
/ 4.8
| 36 | R130R (CGA→CGT) | pdxB | erythronate‑4‑phosphate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (3/2); new base A (31/0); total (34/2) |
| Fisher's exact test for biased strand distribution p-value = 1.59e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.23e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGGATCGCAAAGTAAGGTTTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGATCCCCACCGTACGGTCGTACAGTGAAAA > minE/1522663‑1522770
|
cGGATCGCAAAGTAAGGTTTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTAcc < 1:253607/69‑1 (MQ=255)
cGGATCGCAAAGTAAGGTTTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTAcc < 1:2326346/69‑1 (MQ=255)
cGCAAAGTAAGGTTTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACg > 1:2822016/1‑68 (MQ=255)
cGCAAAGTAAGGTTTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACg > 1:3064402/1‑68 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGAcc > 1:1952338/1‑51 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTAc > 1:1227501/1‑59 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACTAACGCCAAc > 1:1331221/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGccaa > 1:571084/1‑66 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGccaa > 1:481213/1‑66 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGccaa > 1:1506477/1‑66 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:3094252/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2899832/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2925274/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2945289/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2970343/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2715187/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:3159194/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:319134/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:345596/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:580962/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:882151/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2856503/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2651470/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2422330/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:2097926/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1798215/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1774046/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1590387/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1545244/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:14929/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1435703/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1427004/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1297121/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTCCAGTCGCGCCTGTAAACGACGACCAACGTTACAAACGCCAAc > 1:479238/1‑69 (MQ=255)
aaGTAAGGTTTTGATCCCTAAAGCTTACAGTCGCGCCTGTAAACGACGACCAACGTTACCAACGCCAAc > 1:1375094/1‑69 (MQ=255)
cgcgCCTGCAATCGACGTCCAACGTTACCAACGCCCACGATCCCCACCGTACGGTCGTACAGTGaaaa > 1:390993/1‑68 (MQ=255)
|
CGGATCGCAAAGTAAGGTTTTAATCCCTAACGCTTCCAGTCGCGCCTGCAATCGACGTCCAACGTTACCAACGCCCACGATCCCCACCGTACGGTCGTACAGTGAAAA > minE/1522663‑1522770
|
| 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
