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 |
|
A17 F109 I0 R1
|
32 |
27.2 |
584098 |
96.5% |
563654 |
139.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
469,786 |
A→G |
100% |
G118G (GGA→GGG) |
USA300HOU_0445 → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 469,786 | 0 | A | G | 90.7%
| 47.1
/ ‑2.3
| 21 | G118G (GGA→GGG) | USA300HOU_0445 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (9/10); total (10/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GAGATGGCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGAA > CP000730/469650‑469918
|
gataTGGCAAATTTAAAATGGGTTATAAAGGGATGGGGACCATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCat < 1:262755/137‑1 (MQ=21)
gaTGGCGAATTTAAACAGCGTGGTAAAGAGATGCGGACGATATATACAGATTGCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACatta < 2:8995/140‑1 (MQ=255)
tttAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCATAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTaa < 1:81014/140‑1 (MQ=255)
aaaaGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTTGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACa < 1:82721/140‑1 (MQ=255)
aatggTGATAAAGGGATGTGGACGATATATACAAATTTCGCCGAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTATTATACTTAGATAGTAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACAtt < 2:136740/137‑1 (MQ=25)
gggATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTGTTTTGTTAAGAAATTCTATAATAAggg > 1:39452/1‑140 (MQ=255)
tgGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATACTATAATAAGGGCAAAtt > 1:102228/1‑140 (MQ=255)
gACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTcc > 2:130694/1‑140 (MQ=255)
tataCAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAg > 1:59305/1‑140 (MQ=255)
taCAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGaa > 1:281385/1‑140 (MQ=255)
aCAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAACTTCCCAGATAGaaa > 2:81885/1‑140 (MQ=255)
aaGTAATAAACAAGGTGGAGTGAGTAATGAAGGGATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTtg < 2:21719/140‑1 (MQ=255)
cAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGaaaaa < 1:191025/140‑1 (MQ=255)
cAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACATTATTTTGTTAAGACATACTATAATAAGATCAAATACCCAGATAGAAAAAACGATAAAGATAAAAAGaaaaa > 1:24887/1‑140 (MQ=255)
aTTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATaaaa > 1:101855/1‑140 (MQ=255)
ttGAGTTATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAAt < 1:226096/140‑1 (MQ=255)
tGAGTAATGAAGGTATTGTCTTATACTTAGATAGAAATACAAGGAATGCAAAGGGGCATTATTTTGTTAAGACATTCTATAAGAAATACAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAAtt < 1:139361/140‑1 (MQ=21)
tGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCttat < 2:32558/140‑1 (MQ=255)
ggTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCCGATAGAAAAAATTATAAAGTTGAAATGAAAAATGATAAAATTATATTATTAGa > 2:38679/1‑140 (MQ=255)
gttagaAATACACGGACTGCAAAGGGGCATTATTTTGGTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATTATAAAATTATCTTATTAGATAAAGTAGAAGATACaaa < 2:102228/138‑1 (MQ=255)
cAAAGGGGCATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGaa > 2:136131/1‑140 (MQ=255)
|
GAGATGGCGAATTTAAAAAGGGTGATAAAGGGATGTGGACGATATATACAGATTTCGCCAAAAGTAATAAACAAGGTGGATTGAGTAATGAAGGTATGGTCTTATACTTAGATAGAAATACACGGACTGCAAAGGGACATTATTTTGTTAAGACATTCTATAATAAGGGCAAATTCCCAGATAGAAAAAATTATAAAGTTGAAATGAAAAATAATAAAATTATCTTATTAGATAAAGTAGAAGATACAAATCTAAAAAAGAGAATAGAA > CP000730/469650‑469918
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
