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 |
|
A8 F68 I0 R1
|
412 |
52.0 |
1996146 |
94.7% |
1890350 |
135.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP009273 |
4,028,635 |
A→G |
36.4% |
intergenic (+122/‑256) |
hemG → / → rrsA |
protoporphyrin oxidase, flavoprotein/16S ribosomal RNA of rrnA operon |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP009273 | 4,028,635 | 0 | A | G | 36.4%
| 6.8
/ 7.8
| 11 | intergenic (+122/‑256) | hemG/rrsA | protoporphyrin oxidase, flavoprotein/16S ribosomal RNA of rrnA operon |
| Reads supporting (aligned to +/- strand): ref base A (5/2); new base G (2/2); total (7/4) |
| Fisher's exact test for biased strand distribution p-value = 5.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAAGCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCC > CP009273/4028511‑4028657
|
tAAGCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCGGCGGGGTTCTCCTga < 2:476889/140‑1 (MQ=255)
gaaGCATAAAGAATAAAACATGCGCGGTCAGAAAATTATATTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCAATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCGGCGGGGTTCTCCTga < 2:800597/139‑1 (MQ=255)
gCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGtt < 1:652911/130‑1 (MQ=40)
gCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGtt < 1:966157/130‑1 (MQ=40)
gCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGtt > 2:652911/1‑130 (MQ=40)
gCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGtt > 2:966157/1‑130 (MQ=40)
gCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGaa > 1:798854/1‑140 (MQ=39)
cATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAAc > 1:372742/1‑140 (MQ=38)
aTAAAGAATACAAAATGCTCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATCACGCCCTATAATGCGCGACCACTGACACGGACCAACGGCAAACACGCCGCCGGGTCGGCGGGGTTCTCCTgagactc > 1:60921/1‑137 (MQ=11)
aTAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCGGCGGGGTTCTCCTGAGaatc > 1:715754/1‑138 (MQ=255)
aaaGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTcc > 1:731907/1‑140 (MQ=35)
|
TAAGCATAAAGAATAAAAAATGCGCGGTCAGAAAATTATTTTAAATTTCCTCTTGTCAGGCCGGAATAACTCCCTATAATGCGCCACCACTGACACGGAACAACGGCAAACACGCCGCCGGGTCAGCGGGGTTCTCCTGAGAACTCC > CP009273/4028511‑4028657
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
