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 |
1,801,863 |
T→C |
74.0% |
pseudogene (87/882 nt) |
ygaY → |
ECK2675:JW5428:b2681; predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,801,863 | 0 | T | C | 74.0%
| 50.9
/ 14.4
| 46 | pseudogene (87/882 nt) | ygaY | ECK2675:JW5428:b2681; predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (5/7); new base C (11/23); total (16/30) |
| Fisher's exact test for biased strand distribution p-value = 7.26e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01 |
AACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACA > minE/1801797‑1801929
|
aaCCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATaa > 1:2942535/1‑69 (MQ=255)
aaCCGGTTTATTCACAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATaa > 1:716373/1‑69 (MQ=255)
ctcAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGt > 1:2128145/1‑69 (MQ=255)
ctcAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGt > 1:3175326/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:2867646/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:242108/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:2488034/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:2084965/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:1185044/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:1996968/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:1944569/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:2772185/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:1666536/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:1663479/1‑69 (MQ=255)
tcAGTCGTGGCACAAATTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTg > 1:3256070/1‑69 (MQ=255)
ggCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCAc < 1:1238583/69‑1 (MQ=255)
acaAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACtat < 1:1426788/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGGGGCAAAGTGGTTGGCACCATTATg < 1:2539747/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:2411668/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:3220015/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:3244070/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:286221/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:1942151/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:370835/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:2691172/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:468152/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:1518807/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:2528653/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:2248677/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:936019/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGAACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:3366063/69‑1 (MQ=255)
aTTCTGGTTCCACTGGCAGCGACGCTGGCCTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:1536295/69‑1 (MQ=255)
ttCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:1532214/68‑1 (MQ=255)
ttCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:325271/68‑1 (MQ=255)
ttCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:325080/68‑1 (MQ=255)
ttCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:2434563/68‑1 (MQ=255)
ttCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:1636301/68‑1 (MQ=255)
ttCTGGTTCCACTGGCAGCGACGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:1855796/68‑1 (MQ=255)
tCTGGTTCCACTGGCAGCGTCGCTGGCTTCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:2069092/67‑1 (MQ=255)
aGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTggg > 1:2751401/1‑69 (MQ=255)
tCACCGGACAAACGCGGCAAAGTGGTTGGCACCATTATg < 1:550072/39‑1 (MQ=37)
cGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGa < 1:3199014/69‑1 (MQ=255)
cGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGa < 1:2948203/69‑1 (MQ=255)
cGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGa < 1:2707538/69‑1 (MQ=255)
cGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGa < 1:2466904/69‑1 (MQ=255)
gATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACa < 1:2651661/69‑1 (MQ=255)
|
AACCGGTTTATTCTCAGTCGTGGCACAAATTCTGGTTCCGCTGGCAGCGACGCTGGCTTCACCGGATAAACGCGGCAAAGTGGTTGGCACTATTATGAGCGGTCTGCTGTTGGGGATCTTGCTGGCACGGACA > minE/1801797‑1801929
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
