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 |
|
A3 F21 I0 R1
|
61 |
33.6 |
2680365 |
96.0% |
2573150 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,286,501 |
C→A |
100% |
A261S (GCG→TCG) |
yejK ← |
nucleotide associated protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,286,501 | 0 | C | A | 80.0%
| 23.3
/ 9.2
| 20 | A261S (GCG→TCG) | yejK | nucleotide associated protein |
| Reads supporting (aligned to +/- strand): ref base C (1/3); new base A (8/8); total (9/11) |
| Fisher's exact test for biased strand distribution p-value = 5.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACGCAGTGTGCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGCAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAGCTCTTTCGACAGCGATTTCAGTTCGA > W3110S.gb/2286442‑2286563
|
aCGCAGTGTGCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTg < 1:170641/70‑1 (MQ=255)
gCAGTGTGCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAg > 1:1254589/1‑71 (MQ=255)
cAGTGTGCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGCAAACTCCGTGAAGc < 1:1517918/71‑1 (MQ=255)
gtgCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCa > 1:766288/1‑70 (MQ=255)
gtgCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCAc > 1:1109359/1‑71 (MQ=255)
tgCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGCAAACTCCGTGAAGCTCACt > 1:1710045/1‑71 (MQ=255)
tgCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCAc > 1:523486/1‑70 (MQ=255)
tgCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGACGAAAACTCCGTGAAGCTCACt > 1:488043/1‑71 (MQ=255)
cTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGaaaa > 1:2059166/1‑53 (MQ=255)
cTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGaaaa > 1:595820/1‑53 (MQ=255)
cGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACTTCGCt < 1:1113648/71‑1 (MQ=255)
cGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACTTCGCt < 1:361680/71‑1 (MQ=255)
cTGACGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACTTCGCTTACg > 1:2192121/1‑71 (MQ=255)
aaGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGCAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAg < 1:1003379/71‑1 (MQ=255)
tctctTCCAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCa > 1:736127/1‑48 (MQ=255)
ccAGTTCGTAGCCTTTTTCAGCCGCAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAGCTCTTTc < 1:411296/68‑1 (MQ=255)
ccAGTTCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAGCTCTTTc < 1:993124/68‑1 (MQ=255)
ttCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACtt < 1:1749116/41‑1 (MQ=255)
ttCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACtt < 1:944771/41‑1 (MQ=255)
ttCGTAGCCTTTTTCAGCCGAAAACTCCGTGAAGCTCACtt < 1:1397354/41‑1 (MQ=255)
ttttCAGCCGAAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAGCTCTTTCGa > 1:2630172/1‑56 (MQ=255)
tCAGCCGAAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAGCTCTTTCGACAGCGATTTCAGTTCGa < 1:2678376/70‑1 (MQ=255)
|
ACGCAGTGTGCTACGGTCTGCCGGGAAGCTCTCTTCCAGTTCGTAGCCTTTTTCAGCCGCAAACTCCGTGAAGCTCACTTCGCTTACGCCTGCCAGCTCTTTCGACAGCGATTTCAGTTCGA > W3110S.gb/2286442‑2286563
|
| 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
