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 |
|
A1 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,546,724 |
T→C |
12.8% |
S2S (AGT→AGC) |
fimE → |
tyrosine recombinase/inversion of on/off regulator of fimA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,546,724 | 0 | T | C | 12.8%
| 175.8
/ 18.5
| 70 | S2S (AGT→AGC) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA |
| Reads supporting (aligned to +/- strand): ref base T (28/33); new base C (5/4); total (33/37) |
| Fisher's exact test for biased strand distribution p-value = 7.26e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
TTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGG > W3110S.gb/4546655‑4546791
|
ttGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGt > 1:1674754/1‑70 (MQ=255)
tGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTa < 1:1338687/70‑1 (MQ=255)
tGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTa < 1:2694989/70‑1 (MQ=255)
ttGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTa < 1:2750477/63‑1 (MQ=255)
ttGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAcgtcgt < 1:1199027/71‑1 (MQ=255)
gAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTa > 1:1909178/1‑71 (MQ=255)
tttCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCtt < 1:520013/71‑1 (MQ=255)
ggTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTa > 1:323244/1‑69 (MQ=255)
tATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaaga < 1:144109/71‑1 (MQ=255)
attcattcAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaag > 1:1881411/1‑69 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:1397177/71‑1 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:1181952/71‑1 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:814150/71‑1 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:318194/71‑1 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTa > 1:2285481/1‑52 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCt > 1:589068/1‑55 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt > 1:264213/1‑71 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt > 1:635091/1‑71 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCaaa > 1:84068/1‑44 (MQ=255)
attcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTaa < 1:879412/42‑1 (MQ=255)
attcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTaa < 1:88298/42‑1 (MQ=255)
attcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:2486272/68‑1 (MQ=255)
ttcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAcgtc < 1:747942/46‑1 (MQ=255)
ttcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAcgtc < 1:1093506/46‑1 (MQ=255)
ttcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGtt < 1:2756483/49‑1 (MQ=255)
ttcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGtt < 1:2059230/49‑1 (MQ=255)
ttcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaag < 1:1996035/64‑1 (MQ=255)
ttcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaag < 1:2614442/64‑1 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTAc > 1:2688121/1‑54 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag > 1:2809238/1‑65 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg > 1:2325685/1‑71 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg > 1:2755140/1‑71 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg > 1:1778285/1‑71 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCgg > 1:728903/1‑57 (MQ=255)
aaaTATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCTGTAaag < 1:898659/61‑1 (MQ=255)
atatatCTCAGTTAGTAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCa < 1:1633034/71‑1 (MQ=255)
tatatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:96291/71‑1 (MQ=255)
tatatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:1792003/71‑1 (MQ=255)
tatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:2511095/1‑71 (MQ=255)
tatCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatg < 1:2076422/70‑1 (MQ=255)
tatCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatg < 1:2007344/70‑1 (MQ=255)
tcAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatgatg > 1:1580342/1‑69 (MQ=255)
gTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGcc > 1:1347127/1‑60 (MQ=255)
ttAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAaag < 1:142364/48‑1 (MQ=255)
gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt < 1:887679/71‑1 (MQ=255)
gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt < 1:2515606/71‑1 (MQ=255)
gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt < 1:2004185/71‑1 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAaag < 1:2697707/39‑1 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAaag < 1:2268080/39‑1 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTa > 1:100559/1‑70 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc > 1:2212838/1‑71 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc > 1:906996/1‑71 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc > 1:666515/1‑71 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTAc > 1:669806/1‑71 (MQ=255)
actaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACgg > 1:1951080/1‑71 (MQ=255)
actaTTGTGAGCAAACGTCGTTATCTTACCGGTAaag < 1:67240/37‑1 (MQ=255)
ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACggg > 1:2583989/1‑71 (MQ=255)
taTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:1025114/1‑50 (MQ=255)
taTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:1903588/1‑50 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:866795/1‑48 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:1124956/1‑48 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGc < 1:426927/70‑1 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGc > 1:2659322/1‑70 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGc > 1:866725/1‑70 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGc < 1:1813135/70‑1 (MQ=255)
ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:2536028/1‑48 (MQ=255)
ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:232249/1‑48 (MQ=255)
tgAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:673529/43‑1 (MQ=255)
tgAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:415197/43‑1 (MQ=255)
aGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACgg > 1:955064/1‑70 (MQ=255)
aGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACgg < 1:986074/70‑1 (MQ=255)
tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:2788137/39‑1 (MQ=255)
tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:1091048/39‑1 (MQ=255)
|
TTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGG > W3110S.gb/4546655‑4546791
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
