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 F18 I0 R2
|
19 |
23.5 |
523274 |
98.7% |
516471 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
1,576,651 |
A→G |
23.6% |
F289S (TTC→TCC) |
USA300HOU_RS07705 ← |
Glycyl‑glycine endopeptidase ALE‑1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 1,576,651 | 0 | A | G | 23.6%
| 25.3
/ 7.0
| 17 | F289S (TTC→TCC) | USA300HOU_RS07705 | Glycyl‑glycine endopeptidase ALE‑1 |
| Reads supporting (aligned to +/- strand): ref base A (6/7); new base G (2/2); total (8/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01 |
TTAATGCTGCACCTAACCCTAAAGTAATTGGTGTAGATA‑CGCCCATCGTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCTTTATTAACAGCTGTTTCAGCTTTTGCGACATTAGCGC > USA300TCH1516_ALE/1576517‑1576786
|
ttAATGCTGCACCTAACCCTAAAGTAATTGGTGTAGATA‑CGCCCATCGTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGAc < 2:121017/141‑1 (MQ=255)
gcACCTAACCCTAAAGTAATTGGTGTAGATATCGGTGGTCG‑CCGTATAATTAAAAAAGAAATCATTTTGTCTCCAATAGAACTAAATTTCTTTGAAATGACATCCGCTTGACTTGCAAGTTTACCGAAATAACtttatgct > 2:3162/1‑136 (MQ=255)
gcACCTAACCCTAAAGTAATTGGTGTAGATA‑CGCCCATCGTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCt > 1:167177/1‑141 (MQ=255)
aGTAATTGGTGTAGATA‑CGCCCATCGTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCttt < 2:250157/141‑1 (MQ=255)
gTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGaa > 1:15775/1‑141 (MQ=255)
gTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGaa > 1:15662/1‑141 (MQ=255)
cATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGc > 1:221843/1‑141 (MQ=255)
aaGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGGAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCt > 1:99073/1‑141 (MQ=255)
aaGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGGAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCt > 1:98996/1‑141 (MQ=255)
aTAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAagca < 2:221843/141‑1 (MQ=255)
aGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAagcagc < 1:30597/141‑1 (MQ=255)
aaTTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCt < 1:60173/141‑1 (MQ=255)
aaTTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCt < 1:47955/141‑1 (MQ=255)
tttGACATGACATCCACTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCTttatta > 2:79757/1‑141 (MQ=255)
cTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCTTTATTAACAGCTGTTTCAGCTTTTGCg < 2:31946/141‑1 (MQ=255)
tACCGGAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCTTTATTAACAGCTGTTTCAGCTTTTGCGACATTAgcgc < 2:98996/141‑1 (MQ=255)
tACCGGAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCTTTATTAACAGCTGTTTCAGCTTTTGCGACATTAgcgc < 2:99073/141‑1 (MQ=255)
|
TTAATGCTGCACCTAACCCTAAAGTAATTGGTGTAGATA‑CGCCCATCGTCATTGTACGTCCCAGGGAAGTCATTTTGTCTCCAATAGAACTAAATTTCTTTGACATGACATCCGCTTGACTTGCAAGTTTACCGAAATGACTTTGAGCTATCATTTGTTCTTTGTTAAAAGTCTTCATTTCGGATGAAGCTTTATCTATTGAACGCTCCAAATTATTTAAAGCAGCTTTTTCTTTATTAACAGCTGTTTCAGCTTTTGCGACATTAGCGC > USA300TCH1516_ALE/1576517‑1576786
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
