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 |
|
A1 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,061,031 |
A→G |
100% |
Q509R (CAG→CGG) |
yliK → |
methylmalonyl‑CoA mutase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,061,031 | 0 | A | G | 96.8%
| 100.4
/ ‑3.9
| 31 | Q509R (CAG→CGG) | yliK | methylmalonyl‑CoA mutase |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (15/15); total (16/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGCGCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACAGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGTTCGCGCCACCCTG > W3110S.gb/3060970‑3061089
|
cgcgCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACg > 1:1028100/1‑70 (MQ=255)
cgcgCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACg > 1:105130/1‑70 (MQ=255)
cgcgCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACg > 1:2001534/1‑70 (MQ=255)
cgcgCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACg > 1:1480049/1‑70 (MQ=255)
cgcgCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACg > 1:1769349/1‑70 (MQ=255)
cgcgCAACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACg > 1:1159437/1‑70 (MQ=255)
gcgcCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGaa < 1:3640702/71‑1 (MQ=255)
gcgcCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGaa < 1:111613/71‑1 (MQ=255)
gcgcCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGaa < 1:1813852/71‑1 (MQ=255)
ccGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACctgc > 1:2831494/1‑71 (MQ=255)
cGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACctgct > 1:3710696/1‑71 (MQ=255)
cGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACAGCATAACGAAAACctgct > 1:2406711/1‑71 (MQ=255)
ccgTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGtt < 1:1725788/71‑1 (MQ=255)
ccgTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGtt < 1:163409/71‑1 (MQ=255)
ccgTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGtt < 1:1352172/71‑1 (MQ=255)
cgTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGtt < 1:3298701/70‑1 (MQ=255)
aCCGCCGCGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGc > 1:2165759/1‑71 (MQ=255)
gccgcGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAAcc > 1:3265017/1‑46 (MQ=255)
gccgcGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCg > 1:2635517/1‑70 (MQ=255)
gccgcGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGc > 1:1577298/1‑71 (MQ=255)
gccgcGTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGc > 1:3221374/1‑71 (MQ=255)
gcgTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTcg < 1:1102486/71‑1 (MQ=255)
gcgTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTcg < 1:123410/71‑1 (MQ=255)
gcgTTGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTcg < 1:3260278/71‑1 (MQ=255)
ttGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGt < 1:1035469/71‑1 (MQ=255)
ttGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGt < 1:3587416/71‑1 (MQ=255)
ttGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGt < 1:26397/71‑1 (MQ=255)
ttGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGt < 1:2368389/71‑1 (MQ=255)
ttGAACGCCCTGACTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGt < 1:2089562/71‑1 (MQ=255)
cTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGTTCGCGCCACCCTg > 1:2643855/1‑71 (MQ=255)
cTCACGCCGCACGGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGTTCGCGCCACCCTg > 1:161709/1‑71 (MQ=255)
|
CGCGCCACCCGTGATGATGCCGCCGTAACCGCCGCGTTGAACGCCCTGACTCACGCCGCACAGCATAACGAAAACCTGCTGGCTGCCGCTGTTAATGCCGCTCGCGTTCGCGCCACCCTG > W3110S.gb/3060970‑3061089
|
| 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
