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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,546,724 |
T→C |
30.7% |
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 | 30.7%
| 97.8
/ 64.0
| 75 | S2S (AGT→AGC) | fimE | tyrosine recombinase/inversion of on/off regulator of fimA |
| Reads supporting (aligned to +/- strand): ref base T (24/28); new base C (15/8); total (39/36) |
| Fisher's exact test for biased strand distribution p-value = 1.42e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.28e-01 |
TTGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACGG > W3110S.gb/4546655‑4546791
|
ttGACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGt > 1:1466412/1‑70 (MQ=255)
gACCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTaa < 1:2116439/70‑1 (MQ=255)
aCCGATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAc < 1:2431385/71‑1 (MQ=255)
gATTGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAcgtc < 1:2264432/71‑1 (MQ=255)
ttGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAAcgtcgt < 1:1051760/71‑1 (MQ=255)
tGAGGTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAcgtcgt > 1:2976426/1‑70 (MQ=255)
gTTTCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGtt < 1:2293784/67‑1 (MQ=255)
tttCCTATAGGTATTCATTCAAATATATATCAGTTAGGAGTACTACTATTGTGAGTaa < 1:3090204/58‑1 (MQ=255)
tCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAAc > 1:717630/1‑58 (MQ=255)
tCCTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTAc > 1:3905287/1‑71 (MQ=255)
ccTATAGGTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTAcc > 1:1840481/1‑71 (MQ=255)
ggTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTaa < 1:3800068/70‑1 (MQ=255)
gTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaag < 1:1946369/71‑1 (MQ=255)
gTATTCATTCAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTa > 1:402791/1‑68 (MQ=255)
attcattcAAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAaag > 1:821632/1‑69 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTa < 1:1108336/44‑1 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:4102094/71‑1 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaagaa < 1:129869/70‑1 (MQ=255)
ttcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAaag < 1:2275420/68‑1 (MQ=255)
tcattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGt > 1:3454365/1‑71 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt > 1:2513201/1‑71 (MQ=255)
cattcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt > 1:4443013/1‑71 (MQ=255)
attcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGtt < 1:1279600/70‑1 (MQ=255)
attcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGtt > 1:26040/1‑70 (MQ=255)
tcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTAt > 1:3975110/1‑50 (MQ=255)
tcaAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTAt > 1:2813582/1‑50 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTaaa > 1:1790192/1‑40 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTaaa < 1:518867/61‑1 (MQ=255)
caAATATATCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAgg > 1:3330638/1‑71 (MQ=255)
atatatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATcct < 1:1602576/49‑3 (MQ=255)
tatatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCa > 1:2882627/1‑65 (MQ=255)
tatCTCAGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTa > 1:1987250/1‑47 (MQ=255)
aGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAgg > 1:1831422/1‑71 (MQ=255)
aGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAg > 1:4306987/1‑70 (MQ=255)
aGTTAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGATCAGGCCATGATGCAgg > 1:2905713/1‑71 (MQ=255)
ttAGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCa < 1:2707776/67‑1 (MQ=255)
aGGAGTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:980351/1‑61 (MQ=255)
gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt < 1:2977107/71‑1 (MQ=255)
gTACTACTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGt < 1:1620997/71‑1 (MQ=255)
tactacTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGcc < 1:3237842/52‑1 (MQ=255)
tactacTATTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:464896/54‑1 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:309953/1‑54 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatga > 1:2449250/1‑54 (MQ=255)
ctactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGttt > 1:1064023/1‑66 (MQ=255)
tactaTTGTGAGTAAACGTCGTTATCTTACCGGTaaa < 1:3206481/37‑1 (MQ=255)
tactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCa > 1:3974116/1‑45 (MQ=255)
tactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:139136/51‑1 (MQ=255)
tactaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGt < 1:320044/63‑1 (MQ=255)
actaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGtt > 1:848564/1‑42 (MQ=255)
actaTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:2354773/50‑1 (MQ=255)
actaTTGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:3470281/50‑1 (MQ=255)
ctaTTGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACggg > 1:2943384/1‑71 (MQ=255)
taTTGTGAGTAAACGTCGTTATCTTACCGGTAaagaag < 1:1290117/38‑1 (MQ=255)
ttGTGAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGc < 1:373226/70‑1 (MQ=255)
ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGtta > 1:1626623/1‑38 (MQ=39)
ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTc > 1:4383289/1‑39 (MQ=255)
ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCatgat > 1:326392/1‑49 (MQ=255)
ttGTGAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACg > 1:3275023/1‑66 (MQ=255)
tgtgAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTa < 1:2327693/63‑1 (MQ=255)
gtgAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCat < 1:4084255/44‑1 (MQ=255)
gtgAGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAAc > 1:2464716/1‑71 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTc > 1:2915761/1‑37 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCa > 1:4494429/1‑43 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCa > 1:89461/1‑43 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGc > 1:2615352/1‑49 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGc > 1:3043820/1‑49 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGtt > 1:3752474/1‑61 (MQ=255)
gtgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAAc > 1:935751/1‑71 (MQ=255)
tgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGttt < 1:1571710/57‑1 (MQ=255)
tgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTa < 1:3133920/61‑1 (MQ=255)
tgAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAAc < 1:34409/70‑1 (MQ=255)
gAGCAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACgg > 1:4135767/1‑71 (MQ=255)
aGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAg < 1:4287001/36‑1 (MQ=255)
aGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAg < 1:3132888/36‑1 (MQ=255)
aGTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACgg < 1:2910228/70‑1 (MQ=255)
gTAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGTTTGTTACGGGGCAACgg < 1:1927527/69‑1 (MQ=255)
tAAACGTCGTTATCTTACCGGTAAAGGAGTTCAGGCCATGATGCAGGCGGTTTGTTACgg > 1:3608977/1‑60 (MQ=255)
tAAACGTCGTTATCTTACCGGTAAAGAAGTTCAGGCCATGATGCAGGCGGt < 1:1143621/51‑1 (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
