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 |
2,849,359 |
A→G |
100% |
G558G (GGT→GGC) |
yjeP ← |
predicted mechanosensitive channel |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,849,359 | 0 | A | G | 82.3%
| 60.4
/ 3.8
| 39 | G558G (GGT→GGC) | yjeP | predicted mechanosensitive channel |
| Reads supporting (aligned to +/- strand): ref base A (7/0); new base G (3/29); total (10/29) |
| Fisher's exact test for biased strand distribution p-value = 7.80e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCGGGCAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCAAGCCGTAACCCAGCGTCA > minE/2849302‑2849423
|
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1198793/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:616970/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:456787/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:2878719/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:2786483/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:2323530/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:2267117/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:2247199/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1943234/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1924667/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1667180/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1136807/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1249949/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:1253110/68‑1 (MQ=255)
gcgagcAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCaa < 1:131827/68‑1 (MQ=255)
ggCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAg > 1:862621/1‑69 (MQ=255)
ggCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAg > 1:589646/1‑69 (MQ=255)
ggCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAg > 1:122163/1‑69 (MQ=255)
ggCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAg > 1:2690707/1‑69 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGTTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:2664341/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:1292682/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:230688/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:1971130/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:2603551/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:2607618/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:1428427/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:2748091/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:1901401/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:3381999/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGTGCCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:1471452/69‑1 (MQ=255)
gcAAATCATCACTACCCACAGCAGCGGCACGGCGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:3113664/69‑1 (MQ=255)
cAAATCATCACTACCCACAGCAGCGGCACGGTGGCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:1673885/68‑1 (MQ=255)
cacaGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAGCGGATAAGGCCACGCCTcg > 1:1582855/1‑69 (MQ=255)
gcagcGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCa > 1:1821245/1‑69 (MQ=255)
gcagcGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCa > 1:999650/1‑69 (MQ=255)
ggCTGTTACGCCATCACCAATCGCGACCGCCAGCgg < 1:581266/36‑1 (MQ=25)
ttACGCCATCACCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCAAGCCGTAACCCAGCGTCa > 1:292872/1‑69 (MQ=255)
ttACGCCATCACCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCAAGCCGTAACCCAGCGTCa > 1:1218615/1‑69 (MQ=255)
ttACGCCATCACCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCAAGCCGTAACCCAGCGTCa > 1:2893010/1‑69 (MQ=255)
|
GCGGGCAAAGGTGGCGCAAATCATCACTACCCACAGCAGCGGCACGGTGGCCGTTACACCATCGCCAATCGCGACCGCCAGCGGATAAGGCCACGCCTCGCGCAAGCCGTAACCCAGCGTCA > minE/2849302‑2849423
|
| 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
