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 F8 I0 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,142,011 |
T→C |
100% |
F152L (TTC→CTC) |
katE → |
hydroperoxidase HPII(III) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,142,011 | 0 | T | C | 91.3%
| 68.9
/ ‑0.5
| 23 | F152L (TTC→CTC) | katE | hydroperoxidase HPII(III) |
| Reads supporting (aligned to +/- strand): ref base T (2/0); new base C (21/0); total (23/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCCGCTCACGGTTATTTCCAGCCATATAAAAGCTTAAGCGATATTACCAAAGCGGATTTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTC > minE/1141954‑1142065
|
gCCGCTCACGGTTATTTCCAGCCATATAAAAGCTTAAGCGATATTACCAAAGCGGAtt > 1:2024351/1‑58 (MQ=255)
gCCGCTCACGGTTATTTCCAGCCATATAAAAGCTTAAGCGATATTACCAAAGCGGATTTCct > 1:896552/1‑62 (MQ=255)
gCCGCTCACGGTTATTTCCAGCCATATAAAAGCTTAAGCGATATTACCAAAGCGGATTTCct > 1:1755048/1‑62 (MQ=255)
aGCTTAAGCGATATTACCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAg > 1:1741054/1‑58 (MQ=255)
aGCTTAAGCGATATTACCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAg > 1:447396/1‑58 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:2034884/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1338529/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:844668/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:783673/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:648803/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:571524/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:564508/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:452238/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:276170/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:222430/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1457398/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:139520/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1942361/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1936858/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1886146/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1444443/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1572881/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1565749/1‑67 (MQ=255)
aCCAAAGCGGATCTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTc > 1:1563368/1‑67 (MQ=255)
|
GCCGCTCACGGTTATTTCCAGCCATATAAAAGCTTAAGCGATATTACCAAAGCGGATTTCCTCTCAGATCCGAACAAAATCACCCCAGTATTTGTACGTTTCTCTACCGTTC > minE/1141954‑1142065
|
| 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
