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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,255,918 |
C→T |
38.4% |
G538S (GGC→AGC) |
ycgV ← |
predicted adhesin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,255,918 | 0 | C | T | 38.4%
| 76.5
/ 95.0
| 86 | G538S (GGC→AGC) | ycgV | predicted adhesin |
| Reads supporting (aligned to +/- strand): ref base C (30/23); new base T (19/14); total (49/37) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.09e-01 |
CGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAATGT > W3110S.gb/1255849‑1255987
|
cGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGcc > 1:657292/1‑70 (MQ=255)
aTTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCtaacaa > 1:5011570/1‑71 (MQ=255)
cAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATc < 1:1743967/70‑1 (MQ=255)
aGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAg > 1:1253171/1‑71 (MQ=255)
ctactCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAg < 1:2322129/67‑1 (MQ=255)
actCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaa > 1:347494/1‑56 (MQ=255)
actCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCcaa > 1:4420687/1‑56 (MQ=255)
cccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCa > 1:866519/1‑61 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataa > 1:5053784/1‑70 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataa > 1:714281/1‑70 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataa > 1:377506/1‑70 (MQ=255)
ccGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataa > 1:1115053/1‑70 (MQ=255)
gCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCataata > 1:2215410/1‑70 (MQ=255)
gCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCataata > 1:2169252/1‑70 (MQ=255)
gCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCAtaataa < 1:1919902/71‑1 (MQ=255)
tGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATaaa < 1:4406820/70‑1 (MQ=255)
atatTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg < 1:4166630/70‑1 (MQ=255)
atatTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg < 1:4146262/70‑1 (MQ=255)
atatTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAgg < 1:4115684/70‑1 (MQ=255)
atatTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGt < 1:4914422/71‑1 (MQ=255)
atTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTAc > 1:208723/1‑71 (MQ=255)
atTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTAc > 1:4689269/1‑71 (MQ=255)
ttCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCataata < 1:3277546/63‑1 (MQ=255)
cAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAacaaca > 1:4745341/1‑46 (MQ=255)
cAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGt > 1:32806/1‑71 (MQ=255)
cAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGt > 1:3169932/1‑71 (MQ=255)
aaTAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGt < 1:1556937/70‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCtaac < 1:33386/40‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCtaac < 1:1130382/40‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGt < 1:89285/69‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACAt < 1:1321693/45‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCAtaataa < 1:4778588/60‑1 (MQ=255)
aTAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCAtaataa < 1:1487483/60‑1 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAgaa > 1:1961585/1‑47 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCa > 1:1787084/1‑49 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCa > 1:733414/1‑49 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTAc > 1:2484420/1‑71 (MQ=255)
tAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTAc > 1:2894916/1‑71 (MQ=255)
aaaTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTAcc > 1:1909934/1‑71 (MQ=255)
aaaTCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTAcc > 1:2992918/1‑71 (MQ=255)
tCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTa > 1:3407248/1‑66 (MQ=255)
tCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTa > 1:1141424/1‑66 (MQ=255)
tCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTa > 1:2556044/1‑66 (MQ=255)
ccccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGc > 1:3120673/1‑47 (MQ=255)
cccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCa < 1:4108819/71‑1 (MQ=255)
ccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataat < 1:3796095/50‑1 (MQ=255)
ccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataat < 1:2469055/50‑1 (MQ=255)
ccTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCataat < 1:2234300/50‑1 (MQ=255)
cTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAgg < 1:1074957/71‑1 (MQ=255)
ttattattaACGCCATTACCCTCGCTAACAACATCAGc < 1:475457/38‑1 (MQ=255)
ttattattaACGCCATTACCCTCGCTAACAACATCAGc < 1:1108980/38‑1 (MQ=255)
ttattattaACGCCATTACCCTCGCCAACAACATCAg < 1:821731/37‑1 (MQ=255)
ttattattaACGCCATTACCCTCGCCAACAACATCAg < 1:620954/37‑1 (MQ=255)
ttattattaACGCCATTACCCTCGCCAACAACATCAg < 1:2672858/37‑1 (MQ=255)
tattattaACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTtc > 1:1935632/1‑71 (MQ=255)
tattattaACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTtc > 1:1209654/1‑71 (MQ=255)
attattaACGCCATTACCCTCGCCAACAACATCAGCa > 1:3744912/1‑37 (MQ=255)
ttaACGCCATTACCCTCGCTAACAACATCAGCACGCATAATaaa < 1:1213257/44‑1 (MQ=255)
ttaACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTc > 1:2451414/1‑60 (MQ=255)
ttaACGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTc > 1:301035/1‑60 (MQ=255)
ttaACGCCATTACCCTCGCTAACAACATCAGAACGCATAATaaa < 1:3725688/44‑1 (MQ=38)
aaCGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg > 1:325205/1‑44 (MQ=255)
aaCGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg > 1:2139013/1‑44 (MQ=255)
aaCGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg > 1:3665220/1‑44 (MQ=255)
aaCGCCATTACCCTCGCTAACAACATCAGCACGCATAATAAAgg > 1:3507701/1‑44 (MQ=255)
aCGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGtt < 1:708290/71‑1 (MQ=255)
aCGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGtt < 1:3314163/71‑1 (MQ=255)
cGCCATTACCCTCGCCCACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGtt > 1:1393173/1‑70 (MQ=255)
cGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGtt > 1:2097646/1‑70 (MQ=255)
ccATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTaa > 1:3520926/1‑71 (MQ=255)
ccATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTaa > 1:2214534/1‑71 (MQ=255)
ccATTACCCTCGCCAACAACATCAGCACGCATAATAAAGATACTGTTACCGCTCAGGTTCTCTACGTTTaa > 1:3190596/1‑71 (MQ=255)
aTTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGt < 1:650763/44‑1 (MQ=255)
aTTACCCTCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtg < 1:3152047/71‑1 (MQ=255)
aTTACCCTCGCTAACAAAATCAGCACGCATAATAAAGGTACTGTTAc > 1:3472330/1‑47 (MQ=255)
aTTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtg < 1:2835953/71‑1 (MQ=255)
aTTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtg < 1:2099628/71‑1 (MQ=255)
tACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg > 1:1056069/1‑71 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg > 1:4871634/1‑70 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg > 1:2585583/1‑70 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAAtgtg > 1:3827283/1‑70 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTgg > 1:4521116/1‑71 (MQ=255)
aCCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTgg > 1:3444933/1‑71 (MQ=255)
cTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCaa < 1:4687336/71‑1 (MQ=255)
cTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCaa < 1:569845/71‑1 (MQ=255)
cTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCaa < 1:2498455/71‑1 (MQ=255)
tCGCTAACAACATCAGCACGCATAATAAAGGTACTGt < 1:2591898/37‑1 (MQ=255)
tCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGtt > 1:4244871/1‑50 (MQ=255)
tCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGtt > 1:3417559/1‑50 (MQ=255)
tCGCTAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTaa < 1:1169226/62‑1 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTa > 1:3244727/1‑53 (MQ=255)
gCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACg > 1:2688150/1‑55 (MQ=255)
ccAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAAtgt < 1:1722542/71‑1 (MQ=255)
|
CGTGATTACCAGCACTACTCCCGCTGATATTCAATAAATCCCCTTTATTATTAACGCCATTACCCTCGCCAACAACATCAGCACGCATAATAAAGGTACTGTTACCGCTCAGGTTCTCTACGTTTAATGTGGCAAATGT > W3110S.gb/1255849‑1255987
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
