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 |
3,659,825 |
C→T |
33.7% |
M193I (ATG→ATA) |
wzxE ← |
O‑antigen translocase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,659,825 | 0 | C | T | 33.7%
| 103.1
/ 77.5
| 83 | M193I (ATG→ATA) | wzxE | O‑antigen translocase |
| Reads supporting (aligned to +/- strand): ref base C (29/26); new base T (18/10); total (47/36) |
| Fisher's exact test for biased strand distribution p-value = 3.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
TGCCCTGCCAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAACC > W3110S.gb/3659757‑3659893
|
tgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat > 1:2332023/1‑71 (MQ=255)
tgccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat > 1:2207960/1‑71 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAatat < 1:3711095/69‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatg < 1:4575095/70‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatg < 1:2997398/70‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatg < 1:2671543/70‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:3435942/69‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:1986423/69‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:1239406/69‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:656/69‑1 (MQ=255)
ccctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGAAGACACCACGTTTGATCAatat < 1:3871767/69‑1 (MQ=255)
cctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACatgat < 1:317731/71‑1 (MQ=255)
ctgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatgatg > 1:4446574/1‑71 (MQ=255)
tgccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATgg > 1:4476783/1‑71 (MQ=255)
gccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACat < 1:2478552/65‑1 (MQ=255)
ccAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATggcg > 1:1580838/1‑71 (MQ=255)
ccGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:2949237/71‑1 (MQ=255)
gTTATCCCAGCTTGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:4508758/69‑1 (MQ=255)
ttATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAAt > 1:2461565/1‑71 (MQ=255)
cccAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAatat < 1:3060970/52‑1 (MQ=255)
ccAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTacca > 1:3974076/1‑71 (MQ=255)
ccAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTac > 1:2593613/1‑69 (MQ=255)
cAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGaa > 1:4933822/1‑64 (MQ=255)
cAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAAt > 1:1653031/1‑65 (MQ=255)
cAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGAAGGAAt > 1:522018/1‑65 (MQ=255)
gCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTaccac > 1:1076454/1‑69 (MQ=255)
tttCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTac < 1:2001956/60‑1 (MQ=255)
tttCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTac < 1:2311397/60‑1 (MQ=255)
tttCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTac < 1:2174911/60‑1 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:2099164/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:439126/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:4092698/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:2932280/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:3550947/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATatga > 1:1951978/1‑42 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGaa > 1:4787143/1‑54 (MQ=255)
tCAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGa > 1:210789/1‑53 (MQ=255)
cAGATAGCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGa < 1:3606420/70‑1 (MQ=255)
cAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGaa > 1:4934100/1‑71 (MQ=255)
cAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGaa > 1:4913912/1‑71 (MQ=255)
aGATAGCTTAACGGGATGACACCACGTTTGATCAATatgat > 1:2580713/1‑41 (MQ=255)
aGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGaa < 1:2660629/70‑1 (MQ=255)
aGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAAt > 1:3251108/1‑71 (MQ=255)
gATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATc < 1:4780517/71‑1 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAatat < 1:4802421/36‑1 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAatat < 1:3287049/36‑1 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAatat < 1:1742025/36‑1 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAatat < 1:1954879/36‑1 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAACatga > 1:3861949/1‑38 (MQ=255)
aTAGCTTAACGGGATGACACCACGTTTGATCAACatga > 1:2277115/1‑38 (MQ=255)
tAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGa < 1:3206955/48‑1 (MQ=255)
aGCTTAACGGGATGACACCACGTTTGATCAACATGATggc > 1:2864851/1‑40 (MQ=255)
aGCTTAACGGGATGACACAACGTTTGATCAACATGATggc > 1:3341523/1‑40 (MQ=255)
gCTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcg > 1:3320901/1‑71 (MQ=255)
cTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcgc < 1:4742899/71‑1 (MQ=255)
cTTAACGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcgc < 1:4737054/71‑1 (MQ=255)
tAACGGGATGACACCACGTTTGATCAACATGATgg > 1:4834927/1‑35 (MQ=255)
tAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAg > 1:1848747/1‑41 (MQ=255)
aCGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGa < 1:913722/71‑1 (MQ=255)
aCGGGATGACACCACGTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGa < 1:2634332/71‑1 (MQ=255)
gggATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:2523458/38‑1 (MQ=255)
gggATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:4875633/38‑1 (MQ=255)
gggATGACACCACGTTTGATCAACATGATGGCGGCAgg < 1:1640351/38‑1 (MQ=255)
ggATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGAcc > 1:1069621/1‑70 (MQ=255)
gATGACACCACGTTTGATCAACATGATGGCGGCAGGaa > 1:5018245/1‑38 (MQ=255)
tGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGc < 1:4236567/71‑1 (MQ=255)
gACACCACGTTTGATCAACATGATGGCGGCAGGAATTaccac > 1:2509262/1‑42 (MQ=255)
caccacGTTTGATCAACATGATGGCGGCAGGAAtt > 1:3225498/1‑35 (MQ=255)
accacGTTTGATCAATATGATGGCGGCAGGAATTac < 1:4844000/36‑1 (MQ=255)
cgacGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGc > 1:745100/3‑71 (MQ=255)
acGTTTGATCAACATGATGGCGGCAGGAATTACCACCAgcg > 1:477897/1‑41 (MQ=255)
acGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcgc > 1:1718710/1‑54 (MQ=255)
cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcccc > 1:2797520/1‑71 (MQ=255)
cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcccc > 1:4532384/1‑71 (MQ=255)
cGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGcccc > 1:3376680/1‑71 (MQ=255)
gTTTGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGa < 1:4904138/44‑1 (MQ=255)
tttGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg < 1:5146327/42‑1 (MQ=255)
tttGATCAACATGATGGCGGCAGGAATTACCACCAGCGCggg < 1:1277701/42‑1 (MQ=255)
tGATCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGAAACGCCCCTTc > 1:4719469/1‑70 (MQ=255)
tGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCa > 1:3948932/1‑71 (MQ=255)
tGATCAACATGATGGCGGCAGGAATTACCACCA‑‑GCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt < 1:4272056/70‑1 (MQ=255)
aTCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAgcgc < 1:2789908/47‑1 (MQ=255)
aTCAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt < 1:49203/70‑1 (MQ=255)
aTCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt < 1:210228/70‑1 (MQ=255)
aTCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCAt < 1:2475305/70‑1 (MQ=255)
tCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGc < 1:4175535/56‑1 (MQ=255)
cAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCaa > 1:3013313/1‑57 (MQ=255)
cAATATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAc > 1:744353/1‑71 (MQ=255)
cAACATGATGGCGGGAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAc > 1:4238576/1‑71 (MQ=255)
aaCATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAAcc > 1:3049373/1‑71 (MQ=255)
|
TGCCCTGCCAGACCGTTATCCCAGCTGGGTTTCAGATAGCTTAACGGGATGACACCACGTTTGATCAACATGATGGCGGCAGGAATTACCACCAGCGCGGGAATCAGCGCCAGACCCAGCAACGCCCCTTCATAACC > W3110S.gb/3659757‑3659893
|
| 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
