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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,155,146:1 |
+A |
69.4% |
coding (783/870 nt) |
prkB ← |
predicted phosphoribulokinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,155,146 | 1 | . | A | 69.4%
| 116.6
/ 69.8
| 62 | coding (783/870 nt) | prkB | predicted phosphoribulokinase |
| Reads supporting (aligned to +/- strand): ref base . (7/12); new base A (22/21); total (29/33) |
| Fisher's exact test for biased strand distribution p-value = 4.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAATCGTTGCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACATCGCCAGCAGCCAGGGGAAATCGATC > W3110S.gb/4155083‑4155212
|
cAATCGTTGCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTaa < 1:3300473/69‑1 (MQ=255)
aaTCGTTGCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTaa > 1:134348/1‑68 (MQ=255)
aaTCGTTGCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTaa > 1:2429783/1‑68 (MQ=255)
aaTCGTTGCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTaa < 1:1436000/68‑1 (MQ=255)
gCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTg < 1:1926899/69‑1 (MQ=255)
ccAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGAtg > 1:1106963/1‑69 (MQ=255)
ccAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGAtg > 1:222786/1‑69 (MQ=255)
aGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGAtgt > 1:427742/1‑68 (MQ=255)
aGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGAtg > 1:2816821/1‑67 (MQ=255)
agcaTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaat < 1:739959/69‑1 (MQ=255)
agcaTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACt < 1:1008513/48‑1 (MQ=255)
gcaTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg < 1:960221/69‑1 (MQ=255)
gcaTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg < 1:3285340/69‑1 (MQ=255)
gcaTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg < 1:2308749/69‑1 (MQ=255)
gcaTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg < 1:1246771/69‑1 (MQ=255)
caTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatga < 1:2708632/69‑1 (MQ=255)
caTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAaatgaa < 1:612032/69‑1 (MQ=255)
aTAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatga > 1:2322792/1‑68 (MQ=255)
taattaatTCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatga > 1:1314098/1‑67 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:3436726/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:3264190/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:2271475/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc > 1:1390081/1‑39 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc > 1:3496072/1‑39 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:2080798/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:2020779/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:793590/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTAcc < 1:1677673/39‑1 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACg > 1:2051099/1‑47 (MQ=39)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACg > 1:3070683/1‑47 (MQ=39)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAatgaatga > 1:2348833/1‑69 (MQ=255)
attaattCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAg < 1:1203428/69‑1 (MQ=255)
taattCCATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGc < 1:615698/69‑1 (MQ=255)
tCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc < 1:1287574/69‑1 (MQ=255)
ccATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg < 1:1324360/57‑1 (MQ=255)
ccATTGCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg < 1:50479/57‑1 (MQ=255)
ccATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc > 1:2620854/1‑68 (MQ=255)
ccATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc > 1:1521710/1‑68 (MQ=255)
ccATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc > 1:3484608/1‑68 (MQ=255)
gCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGa > 1:2860223/1‑41 (MQ=38)
gCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGa > 1:3285805/1‑41 (MQ=38)
gCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGa > 1:3565131/1‑41 (MQ=38)
gCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGa > 1:3595746/1‑41 (MQ=38)
gCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGa > 1:688695/1‑41 (MQ=38)
gCCAGACCCATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACAt > 1:2675196/1‑69 (MQ=255)
gCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAaatg > 1:1358589/1‑51 (MQ=255)
aGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACATCg < 1:2525595/67‑1 (MQ=255)
ccATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGa > 1:1629231/1‑41 (MQ=38)
ccATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGa < 1:3303897/41‑1 (MQ=38)
ccATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGa < 1:1354491/41‑1 (MQ=38)
ccATTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGa > 1:2911209/1‑41 (MQ=38)
aTTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc < 1:50778/55‑1 (MQ=255)
aTTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc < 1:2475461/55‑1 (MQ=255)
aTTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc < 1:888518/55‑1 (MQ=255)
aTTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc > 1:2677860/1‑55 (MQ=255)
aTTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc > 1:2027196/1‑55 (MQ=255)
aTTTTGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGc < 1:3295585/55‑1 (MQ=255)
ttttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTG‑GACATCGCCAGCAGcc < 1:3049737/69‑1 (MQ=255)
ttttGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGa < 1:503680/37‑1 (MQ=255)
ttttGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGa < 1:2224428/37‑1 (MQ=255)
ttttGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACATCGCCAGCAGcc < 1:3056067/69‑1 (MQ=255)
tttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACATCGCCAGCAGcc < 1:2444240/69‑1 (MQ=255)
tttGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGa < 1:535638/36‑1 (MQ=255)
ttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatga > 1:2138871/1‑41 (MQ=38)
ttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatga > 1:2823500/1‑41 (MQ=38)
ttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAaatg > 1:831386/1‑40 (MQ=38)
ttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAg < 1:127364/46‑1 (MQ=39)
ttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAg < 1:2219032/46‑1 (MQ=39)
ttGCCGCCCGGTACCAACTAACGTATTGATGTGGGAAATGAATGAg < 1:3262557/46‑1 (MQ=39)
ccgccCGGTACC‑ACTAACGTATTGATGTGGGAaatgaa < 1:814323/38‑1 (MQ=255)
aCC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACATCGCCAGCAGCCAGGGGAAATCGATc > 1:2328417/1‑69 (MQ=255)
|
CAATCGTTGCACCAGCGGCAGCATAATTAATTCCATTGCCAGACCCATTTTGCCGCCCGGTACC‑ACTAACGTATTGATGTGGGAAATGAATGAGCCTTGCAACATCGCCAGCAGCCAGGGGAAATCGATC > W3110S.gb/4155083‑4155212
|
| 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
