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 |
|
A61 F1 I1 R1
|
19 |
50.7 |
3232285 |
96.8% |
3128851 |
74.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,619,387 |
C→A |
intergenic (‑5/+20) |
tadA ← / ← yfhB |
tRNA‑specific adenosine deaminase/hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,619,387 | 0 | C | A | 97.1%
| 129.2
/ ‑3.0
| 35 | intergenic (‑5/+20) | tadA/yfhB | tRNA‑specific adenosine deaminase/hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (16/18); total (17/18) |
| Fisher's exact test for biased strand distribution p-value = 4.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.19e-01 |
TCCAGTATTCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATACACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGATGCTGA > REL606/2619316‑2619458
|
tCCAGTATTCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACg < 2:1314857/75‑1 (MQ=255)
tCCAGTATTCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACg > 1:78452/1‑75 (MQ=255)
ccAGTATTCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACgg < 2:14135/75‑1 (MQ=255)
cAGTATTCGTAGCTAAACTCGACATCAGACAAAAAGAACACTCCGGAAATAAAAGCGCGGCGCATTATAAACGGa < 2:175581/75‑1 (MQ=255)
ttCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTa > 1:1048924/1‑75 (MQ=255)
ttCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTa > 1:1196985/1‑75 (MQ=255)
ttCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTa < 1:852141/75‑1 (MQ=255)
ttCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTa > 1:299107/1‑75 (MQ=255)
cTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTa > 2:513431/1‑75 (MQ=255)
cTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTa < 1:733702/75‑1 (MQ=255)
tCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTAt > 1:795666/1‑75 (MQ=255)
cGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTAtt < 2:480444/75‑1 (MQ=255)
aCTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTcc > 2:430176/1‑75 (MQ=255)
aCTTCAGACAAAAAGAAAACTCCGGTTAT‑AAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCa < 1:922418/75‑1 (MQ=255)
cAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCGATTCCAGtt < 2:635569/75‑1 (MQ=255)
aCAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCt < 1:244106/75‑1 (MQ=255)
cAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTg < 1:1171277/75‑1 (MQ=255)
gAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTc < 1:179533/75‑1 (MQ=255)
gAAAACTCCGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTc > 2:990158/1‑75 (MQ=255)
cGGTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACcgcgcg > 1:1288666/1‑75 (MQ=255)
ggTTATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCgg < 1:1305715/75‑1 (MQ=255)
ttATAAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCgggg > 1:624100/1‑75 (MQ=255)
tataAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGt > 1:978493/1‑75 (MQ=255)
tataAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGt > 2:1276240/1‑75 (MQ=255)
taAAAGCGCGGCGCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTa > 1:68524/1‑75 (MQ=255)
gcggcgCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCa > 1:193482/1‑75 (MQ=255)
cggcgCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCaa < 2:1114281/75‑1 (MQ=255)
cggcgCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCaa < 2:229222/75‑1 (MQ=255)
ggcgCATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAAc > 1:540374/1‑75 (MQ=255)
gcgcATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACg > 1:218031/1‑75 (MQ=255)
cgcATTATACACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGa > 1:1104816/1‑75 (MQ=255)
cgcATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGa < 2:109230/75‑1 (MQ=255)
cgcATTATAAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGa < 1:845831/75‑1 (MQ=255)
ataAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGATGCTGa < 1:1037935/75‑1 (MQ=255)
ataAACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGATGCTGa < 2:768613/75‑1 (MQ=255)
|
TCCAGTATTCGTGGCTAAATTCGACTTCAGACAAAAAGAAAACTCCGGTTATAAAAGCGCGGCGCATTATACACGGACGCTATGCTTTACTCTATTCCAGTTGCTGGAGTTCACCGCGCGGGGTTACTCGCCAACGATGCTGA > REL606/2619316‑2619458
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
