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 |
|
A5 F17 I0 R1
|
87 |
56.5 |
4283937 |
98.6% |
4223961 |
62.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,544,435 |
A→G |
10.8% |
intergenic (‑252/‑1204) |
yjhA ← / → fimB |
N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,544,435 | 0 | A | G | 10.8%
| 93.8
/ 4.9
| 37 | intergenic (‑252/‑1204) | yjhA/fimB | N‑acetylnuraminic acid outer membrane channel protein/tyrosine recombinase/inversion of on/off regulator of fimA |
| Reads supporting (aligned to +/- strand): ref base A (14/19); new base G (2/2); total (16/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
GAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCTGTTGATCTCATTTT > W3110S.gb/4544366‑4544497
|
gagaTCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCtat < 1:1333106/71‑1 (MQ=255)
agaTCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCtata > 1:813296/1‑71 (MQ=255)
aTCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATc < 1:2501043/71‑1 (MQ=255)
cAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACt > 1:2069755/1‑71 (MQ=255)
ccTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCa > 1:4039663/1‑71 (MQ=255)
gAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCaa > 1:1234809/1‑64 (MQ=255)
tataAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTAc > 1:3721512/1‑71 (MQ=255)
taAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCtat < 1:3699883/46‑1 (MQ=255)
taAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTAcc < 1:2724734/70‑1 (MQ=255)
aaaTCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTatat > 1:2231462/1‑46 (MQ=255)
ctctTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATc < 1:2062953/43‑1 (MQ=255)
tcttctGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCa > 1:2181602/1‑71 (MQ=255)
ttctGATGTTTAATTGATTTGAATGTTCGTAAGCTGTATCACTTACTCAATCCATTTTACCCAGAGTCa > 1:771410/1‑69 (MQ=255)
ttctGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCa < 1:648918/63‑1 (MQ=255)
ttctGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTc < 1:3173814/68‑1 (MQ=255)
ttctGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCAt > 1:2810366/1‑70 (MQ=255)
tGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAAt < 1:2167551/45‑1 (MQ=255)
tGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAg < 1:3806093/71‑1 (MQ=255)
tAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAAt > 1:3820143/1‑70 (MQ=255)
tAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAAt < 1:3476289/70‑1 (MQ=255)
tAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATg > 1:1576571/1‑71 (MQ=255)
aTTGATTTGAATGTTCGTAAGCTGTATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGt < 1:1438071/70‑1 (MQ=255)
aTTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATaa < 1:3158038/60‑1 (MQ=255)
aTTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGt < 1:1182920/70‑1 (MQ=255)
ttGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCt < 1:3237085/71‑1 (MQ=255)
ttGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCt < 1:128738/71‑1 (MQ=255)
ttGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCTGTTGa > 1:3177812/1‑71 (MQ=255)
aaTGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCa < 1:67519/42‑1 (MQ=255)
aaTGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATaa < 1:3967489/51‑1 (MQ=255)
aaTGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCTGTTGAtct < 1:3881403/71‑1 (MQ=255)
tGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAAt > 1:2320754/1‑52 (MQ=255)
gTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATa < 1:3026244/52‑1 (MQ=255)
gTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATa < 1:3021263/52‑1 (MQ=255)
ttCGTAAGCTGTATCACTTACTCAATCCATTTTACCCa < 1:3157995/38‑1 (MQ=255)
ttCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCTGTTGATCTCAtt > 1:3756284/1‑71 (MQ=255)
tCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATaaaa > 1:2547508/1‑48 (MQ=255)
tCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATaaaa > 1:1786243/1‑48 (MQ=255)
cGTAAGCTGTATCACTTACTCAATCCATTTTACCCaga > 1:1061261/1‑38 (MQ=255)
gTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATa < 1:3069356/48‑1 (MQ=255)
gTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATa < 1:4187820/48‑1 (MQ=255)
gTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCTGTTGATCTCAtttt > 1:471879/1‑70 (MQ=255)
atatCACTTACTCAATCCATTTTACCCAGAGTCATaaa > 1:2364657/1‑38 (MQ=255)
atatCACTTACTCAATCCATTTTACCCAGAGTCATaaa > 1:2874757/1‑38 (MQ=255)
|
GAGATCCAGATTAAATACCTGAGTATAAAATCTCTTCTGATGTTTAATTGATTTGAATGTTCGTAAGCTATATCACTTACTCAATCCATTTTACCCAGAGTCATAAAATAGAATGTCTGTTGATCTCATTTT > W3110S.gb/4544366‑4544497
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
