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 |
|
A19 F106 I0 R1
|
35 |
30.0 |
670850 |
95.5% |
640661 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,335,371 |
A→G |
21.2% |
L117P (CTA→CCA) |
USA300HOU_RS11915 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,335,371 | 0 | A | G | 21.2%
| 26.0
/ 5.4
| 19 | L117P (CTA→CCA) | USA300HOU_RS11915 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (10/5); new base G (2/2); total (12/7) |
| Fisher's exact test for biased strand distribution p-value = 6.03e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.96e-01 |
GATTAAAAATAAACATAAAATAAGTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCTTGATTGGATATAGCTTT > USA300TCH1516_ALE/2335231‑2335504
|
aaatAAAAATAAACATAAAATAAGTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTa < 2:64170/138‑1 (MQ=255)
aaCATAAAATAAGTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGAcat > 1:88761/1‑139 (MQ=255)
aaaaTAAGTAGAAAAATAAACGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTGTTAAAAGCTGGCCATAGACCTCTatc > 1:201631/1‑141 (MQ=255)
aaaaTAAGTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTGGCCATAGACCTCTatc > 1:62868/1‑141 (MQ=255)
aaGTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATACCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCCCTATcatcat > 2:77392/1‑141 (MQ=255)
aaGTAGAAAAAGAAAAGCTACGAATATTAAAAAATTAGATTTCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCTCTATcatcat < 2:113938/141‑1 (MQ=255)
gTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCTCTATCATCatat < 1:316668/141‑1 (MQ=255)
aaTAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATCGACCTCTATCATCATATAAATGat > 2:51864/1‑141 (MQ=255)
aaaTATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAACATTTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGtttt < 1:260470/140‑1 (MQ=255)
aaaaaaTGTGATATCTTGATTCTCAAATTCCGATATTAAACCATTATATTTTTCAGAATATCTTGCATGATCTTCATTATTATTAAAAGCTAGCCATCGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTAtt < 2:81795/141‑1 (MQ=255)
ttATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCa > 2:237504/1‑141 (MQ=255)
aaaTTCCGATATTAAATCATTATATTTTTCTGTATTTTTTGCATAATCTTCATTATTATTAAAATCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTTTTAATTATATATATTTCaaattt > 2:126850/1‑136 (MQ=255)
atCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCTCTATCATCATATAAATGATCTATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAAACCtt > 2:53064/1‑141 (MQ=255)
aaTCTTCATTATTATTAAAAGCTGGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCtt < 2:201631/141‑1 (MQ=255)
aaTCTTCATTATTATTAAAAGCTGGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCtt < 2:62868/141‑1 (MQ=255)
tCTTCATTATTTTTAAAAGCTAAACGCAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCTTGa > 1:161232/1‑141 (MQ=255)
cTTCATTATTATTAAAAGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGACATTTCCAAGTAACACTTTAAAGTGGTGAt > 2:335258/1‑141 (MQ=255)
attattaAAAGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCTTGATTGGatat > 1:164902/1‑141 (MQ=255)
ttaAAAGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCTTGATTGGATATAGCt > 1:324258/1‑141 (MQ=255)
aaaaGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCTTGATTGGATATAGCttt < 1:63640/141‑1 (MQ=255)
|
GATTAAAAATAAACATAAAATAAGTAGAAAAATAAAAGCTACGAATATTAAAAAATTAGATATCTTCATTATCAAATTCCGATATTAAATCATTATATTTTTCAGAATATCTTGCATAATCTTCATTATTATTAAAAGCTAGCCATAGACCTCTATCATCATATAAATGATATATTAAGTTTTTAGTATTGTTAATTATATATATTTCAGAATAATTATCATTCTGATTGATATTTGGAACTAACCCTTTAAAGTCTTGATTGGATATAGCTTT > USA300TCH1516_ALE/2335231‑2335504
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
