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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,276,691 |
Δ1 bp |
100% |
coding (994/1815 nt) |
yejA → |
predicted oligopeptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,276,691 | 0 | T | . | 83.3%
| 121.5
/ 25.6
| 42 | coding (994/1815 nt) | yejA | predicted oligopeptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (7/0); new base . (20/15); total (27/15) |
| Fisher's exact test for biased strand distribution p-value = 3.82e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
GGCTGGCGTTTAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGTTA > W3110S.gb/2276623‑2276752
|
ggctggcGTTTAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCct > 1:3031700/1‑69 (MQ=255)
ggcGTTTAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCcttgac > 1:2407974/1‑66 (MQ=255)
tttAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg < 1:3357699/69‑1 (MQ=255)
tttAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCctttgactt > 1:679978/1‑68 (MQ=255)
ttAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCctttgactttg < 1:2555683/69‑1 (MQ=255)
ttAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCctttgactttg < 1:698727/69‑1 (MQ=255)
tAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCctttgactttga > 1:3110170/1‑69 (MQ=255)
cAACGTCCGGTATTCAGCGCTCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATg > 1:3026049/1‑68 (MQ=255)
cAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg < 1:345840/60‑1 (MQ=255)
cAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg < 1:2171321/60‑1 (MQ=255)
cAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg < 1:507824/60‑1 (MQ=255)
cAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGa < 1:1169708/69‑1 (MQ=255)
gTCGGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATg < 1:2049372/60‑1 (MQ=255)
cGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACAAgg > 1:681056/1‑69 (MQ=255)
ttCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACAAGGCgttg > 1:3275206/1‑69 (MQ=255)
ttCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACAAGGCgttg > 1:3686479/1‑69 (MQ=255)
tCAGCGATCGCCGGGTCCGTGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCgttgt < 1:310238/68‑1 (MQ=255)
tCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCgttgt < 1:1865787/68‑1 (MQ=255)
tCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCgttgt < 1:1484622/68‑1 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCctttgact > 1:3630403/1‑44 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCctttgact > 1:2797118/1‑44 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACa > 1:2519247/1‑59 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACAAGGCgttgt > 1:2241904/1‑68 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGTATGAACAAGGCGTTGttt < 1:488967/69‑1 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCgttgtt > 1:3536052/1‑68 (MQ=255)
cAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGttt > 1:3018183/1‑69 (MQ=255)
cGATCGCCGGGTCCGTGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTAc < 1:360635/69‑1 (MQ=255)
cGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGTATGAACAAGGCGTTGTTTTa < 1:2017163/68‑1 (MQ=255)
cGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGGTGAACAAGGCGTTGTTTTAc < 1:718055/69‑1 (MQ=255)
cGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTa < 1:244780/68‑1 (MQ=255)
cGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTAc < 1:2233826/69‑1 (MQ=255)
cGATCGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTAc < 1:1051932/69‑1 (MQ=255)
cGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg > 1:2092730/1‑39 (MQ=38)
cGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg < 1:148395/39‑1 (MQ=38)
cGCCGGGTCCGGGAAGCTATCACTCTCGcc‑ttgactttg < 1:876148/39‑1 (MQ=38)
cGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAAt > 1:1880477/1‑68 (MQ=255)
cGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAAt > 1:1567966/1‑68 (MQ=255)
cGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATg > 1:1068319/1‑69 (MQ=255)
cGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATg > 1:742372/1‑69 (MQ=255)
cGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATg > 1:838375/1‑69 (MQ=255)
cGCCGGGTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATg > 1:3337334/1‑69 (MQ=255)
gggTCCGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGcc > 1:3606685/1‑67 (MQ=255)
ccGGGAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGt > 1:712166/1‑69 (MQ=255)
gggAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCg > 1:1154456/1‑69 (MQ=255)
gggAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCg > 1:2526450/1‑69 (MQ=255)
gggAAGCTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCg > 1:830565/1‑69 (MQ=255)
cTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGaa < 1:3007162/69‑1 (MQ=255)
cTATCACTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGaa < 1:1317528/69‑1 (MQ=255)
aCTCTCGCCTTTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTg > 1:2167467/1‑53 (MQ=255)
aCTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGttt > 1:3659011/1‑41 (MQ=38)
aCTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGttt > 1:2128058/1‑41 (MQ=38)
aCTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGttt > 1:1632618/1‑41 (MQ=38)
aCTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGtt > 1:977366/1‑69 (MQ=255)
aCTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGtt > 1:1898150/1‑69 (MQ=255)
aCTCTCGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGtt > 1:3207543/1‑69 (MQ=255)
ctctCGCCTTTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGtt > 1:1387241/1‑69 (MQ=255)
tctcGCC‑TTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGTTa < 1:1140433/68‑1 (MQ=255)
tttgactttgaATGGATGAACAAGGCGTTGTTTTAc < 1:390546/36‑1 (MQ=255)
|
GGCTGGCGTTTAATATCCAACGTCCGGTATTCAGCGATCGCCGGGTCCGGGAAGCTATCACTCTCGCCTTTGACTTTGAATGGATGAACAAGGCGTTGTTTTACAATGCCTGGAGTCGCACGAACAGTTA > W3110S.gb/2276623‑2276752
|
| 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
