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 |
1,015,889 |
G→A |
63.3% |
F60F (TTC→TTT) |
fumA ← |
aerobic Class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,015,889 | 0 | G | A | 63.3%
| 25.2
/ 28.3
| 49 | F60F (TTC→TTT) | fumA | aerobic Class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base G (3/15); new base A (25/6); total (28/21) |
| Fisher's exact test for biased strand distribution p-value = 1.72e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
CTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCAAAATCT > minE/1015835‑1015956
|
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGCCGCAGCATAAATGACGcatcat > 1:1689740/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1117182/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:2594463/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:831154/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:811869/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:2258868/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:2230705/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:476474/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:2091616/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:2024521/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1967066/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1958393/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1949422/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:526216/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:553278/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:58768/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:598121/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1756296/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1734874/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:615232/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:139194/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1195511/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCCGACGCAGCATAAATGACGcatcat > 1:2193735/1‑68 (MQ=255)
cTCCGGGTCACGCAGAATGTCGGCCACCCGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:1896681/1‑68 (MQ=255)
cTCCGGGTCAAGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGcatcat > 1:726123/1‑68 (MQ=255)
tCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGa < 1:3034604/69‑1 (MQ=255)
tCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGa < 1:239805/69‑1 (MQ=255)
tCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGa < 1:2745310/69‑1 (MQ=255)
tCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGa < 1:260649/69‑1 (MQ=255)
tCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGa < 1:1694871/69‑1 (MQ=255)
tCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGAAGCAGCATGAACGACGCATCATGa < 1:1941152/69‑1 (MQ=255)
tCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGa < 1:1943248/63‑1 (MQ=255)
cACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGCATCATGAAACGCCt < 1:1665199/69‑1 (MQ=255)
cACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGCATCATGAAACGCCt < 1:2588783/69‑1 (MQ=255)
cACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGCATCATGAAACGCCt < 1:1797962/69‑1 (MQ=255)
cACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGCATCATGAAACGCCt < 1:1060286/69‑1 (MQ=255)
cACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGCATCATGAAACGCCt < 1:3352350/69‑1 (MQ=255)
cACGCAGAATGTCGGCCACCTGTTGTTGGTGAGCCGGACGCAGCATAAATGACGCATCATGAAACGCCt < 1:1837099/69‑1 (MQ=255)
gttgGTGCGCCGGACGCAGCATGAACGACGCATCATGa > 1:2774131/1‑38 (MQ=255)
gttgGTGCGCCGGACGCAGCATGAACGACGCATCATGa > 1:801532/1‑38 (MQ=255)
gttgGTGCGCCGGACGCAGCATGAACGACGCATCATGa > 1:2966635/1‑38 (MQ=255)
ccGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCg < 1:2159108/68‑1 (MQ=255)
agcaTGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCaaa < 1:3037983/69‑1 (MQ=255)
agcaTGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCaaa < 1:2818373/69‑1 (MQ=255)
gcaTGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCaaa < 1:3150348/68‑1 (MQ=255)
tGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCAAAAtct < 1:866815/69‑1 (MQ=255)
tGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCAAAAtct < 1:472466/69‑1 (MQ=255)
tGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCAAAAtct < 1:3200007/69‑1 (MQ=255)
tGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCAAAAtct < 1:2403826/69‑1 (MQ=255)
|
CTCCGGGTCACGCAGAATGTCGGCCACCTGTTGTTGGTGCGCCGGACGCAGCATGAACGACGCATCATGAAACGCCTGGCGCGCCAACAGAGTTAACGCTTCGGGTGCGACTTTCAAAATCT > minE/1015835‑1015956
|
| 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
