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 |
|
A15 F116 I0 R1
|
44 |
26.4 |
562224 |
96.5% |
542546 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
2,679,708 |
G→A |
64.6% |
W64* (TGG→TGA) |
USA300HOU_2536 → |
possible secretory antigen |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,679,708 | 0 | G | A | 64.6%
| 15.6
/ 11.8
| 22 | W64* (TGG→TGA) | USA300HOU_2536 | possible secretory antigen |
| Reads supporting (aligned to +/- strand): ref base G (3/5); new base A (8/6); total (11/11) |
| Fisher's exact test for biased strand distribution p-value = 6.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTT > CP000730/2679584‑2679825
|
cTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAAtt < 2:102308/141‑1 (MQ=255)
aaTCCGTCGAATAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTAtt < 2:79970/141‑1 (MQ=255)
cGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGATATTACAATGc > 1:74708/1‑141 (MQ=255)
gAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACaaggga > 1:73608/1‑137 (MQ=255)
gCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATc > 1:167682/1‑141 (MQ=255)
attcaTCGCATGCCGCAGTTAATTGTTAGAGTAAAGACCAAATCACATGGTGTGTATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCaa < 1:106245/137‑1 (MQ=255)
aTCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGGTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAAtacaagta > 1:50197/1‑134 (MQ=255)
gCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGc < 2:47635/141‑1 (MQ=255)
aTGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTTGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGGATTACAATGCAGGTAAATGAAAATATgaga > 2:105779/1‑141 (MQ=255)
tattatAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAGAAATTGGTATTACAATGCACGTAACTAAAAATATGGCACTGGCCGTACAC‑Ca > 2:38650/1‑141 (MQ=255)
ccAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGGCGGTAAACCTGTTGCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGt < 2:4522/141‑1 (MQ=255)
ccAATGTACAGGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATAGGGCAATGCTAAAAATTAGTCGTACAATGCACGTAAATCAAAATATGAGACTGGTAGT‑CACACAAGAAACGTTGcagg > 2:37007/1‑138 (MQ=255)
aTGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCGGTCAt > 2:145611/1‑141 (MQ=255)
cATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAAt < 1:165430/141‑1 (MQ=255)
cATGGTGGGCAATTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAAt < 2:158892/141‑1 (MQ=255)
aaTTTCAACGTGGCGCAAAAGTCGGTCACTCTTTTGCGAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGGAAATCAAAAGATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAg < 1:244051/140‑1 (MQ=255)
tAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGata > 2:177111/1‑141 (MQ=255)
aCGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGAtattt > 1:94667/1‑140 (MQ=255)
caAGTCGGTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc < 1:197942/141‑1 (MQ=255)
caAGTCGGTAAACCTGTTTCTAAGAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc < 2:229046/141‑1 (MQ=255)
caAGGCGGTAAACCGGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTc < 2:229054/141‑1 (MQ=255)
ggTAAACCTGTTTCTAATAGATGAGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTAGccgat > 1:130964/1‑137 (MQ=255)
|
CTTATCAATCCGTCGAACAAACGCATCAATCGCATGCCGCAGTTAATTATTATAGTAAAAACCAATGTACATGGTGGGCATTTAAACGTCGCGCACAAGTCGGTAAACCTGTTTCTAATAGATGGGGCAATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACAC‑CAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTT > CP000730/2679584‑2679825
|
| 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
