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 |
|
A23 F43 I1 R1
|
11 |
20.8 |
477872 |
94.5% |
451589 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,372,753 |
+T |
coding (1023/1335 nt) |
pbuG ← |
Guanine/hypoxanthine permease PbuG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,372,752 | 1 | . | T | 95.7%
| 62.4
/ ‑3.4
| 23 | coding (1024/1335 nt) | pbuG | Guanine/hypoxanthine permease PbuG |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (10/12); total (11/12) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAA‑TAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGA > USA300TCH1516_ALE/2372616‑2372887
|
gCTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAA‑ttag > 2:63966/1‑138 (MQ=255)
cTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAACGAACAGCGCTAA‑ttagg > 1:83235/1‑137 (MQ=255)
ggCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAACGTTTGCAGCCATTACTCCACCTACCCCCACTAAGGCTGGTCTCGTAACTCCACTTGTTACCACAGCGATTAACAGGCTAAAGAACAGGGCTAA‑TTGGgaa > 2:225758/1‑141 (MQ=255)
cAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTAGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAGGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGc > 1:158185/1‑141 (MQ=255)
ctttATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCaa < 2:222100/140‑1 (MQ=255)
ctcAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTg > 2:11041/1‑141 (MQ=255)
aGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTc > 2:212786/1‑141 (MQ=255)
aGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTc > 2:212731/1‑141 (MQ=255)
gCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCt < 1:170189/141‑1 (MQ=255)
gCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCt < 1:182123/141‑1 (MQ=255)
gttGCAGCCATTAATACAGATAGTACCACTAAGGGTGGGGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACCGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCAcc < 2:126498/140‑1 (MQ=255)
cATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCaa < 2:97310/141‑1 (MQ=255)
tACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTCGCACCTCCAGCGACACCTg > 1:28665/1‑141 (MQ=255)
tACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTg > 2:195943/1‑141 (MQ=255)
cTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATaagaa < 1:48264/141‑1 (MQ=255)
tGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATaagaag < 2:40250/141‑1 (MQ=255)
tgtCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAgttg < 1:197190/141‑1 (MQ=255)
tCGGAACTGCAGTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAGCAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAgttgtt < 1:224256/141‑1 (MQ=255)
cTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTCTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAgtt < 1:120490/141‑1 (MQ=255)
ttAACGGACTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACa > 2:113073/1‑141 (MQ=255)
aCTAAAGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATACTACAATCGTAg > 1:179794/1‑141 (MQ=255)
aaGAACAGCGCTAATTAGGAAACAACAACCTGTTACGATCCTCGCAAATCCTGATTTAGACCATGCCCGAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTaa > 1:113231/1‑141 (MQ=255)
aaNAGCGCTAATTAGGAAACAACACACTCTGGTCTTGCGATCAAATCCTGTTATGGGACCGACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGa < 1:150124/141‑1 (MQ=255)
aaCAGCGCTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGa < 1:220558/141‑1 (MQ=255)
gcTAATTAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTga > 1:167107/1‑141 (MQ=255)
|
GCTGGCACTGCAACTTCAAAACTTTTCCAGTTTATCTCAGCAAAGTTTGCAGCCATTAATACACCTACCACCACTAAGGCTGGTGTCGTAACTGCACTTGTTACAACAGCGATTAACGGACTAAAGAACAGCGCTAA‑TAGGAAACAACAACCTGTTACGATACTAGCAAATCCTGTTCTAGCACCTACAGCAACACCTGAAGTTGATTCGATATAAGAAGTTGTTGTAGTTGTTCCAAAAACTGATCCTACAATCGTAGCTAAAGAATCTGA > USA300TCH1516_ALE/2372616‑2372887
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
