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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,207,231 |
T→C |
43.8% |
S78S (TCT→TCC) |
manY → |
mannose‑specific enzyme IIC component of PTS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,207,231 | 0 | T | C | 43.8%
| 14.7
/ 56.6
| 73 | S78S (TCT→TCC) | manY | mannose‑specific enzyme IIC component of PTS |
| Reads supporting (aligned to +/- strand): ref base T (11/30); new base C (20/12); total (31/42) |
| Fisher's exact test for biased strand distribution p-value = 3.88e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTGGAAATGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAGGTATCGCACTGGC > minE/1207163‑1207293
|
cTGGAAATGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCt > 1:521303/1‑69 (MQ=255)
aaTGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTTTATCAt < 1:2897/69‑1 (MQ=255)
aaTGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATc < 1:67082/67‑1 (MQ=255)
aaTGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCAt < 1:1664202/69‑1 (MQ=255)
aaTGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCAt < 1:3270494/69‑1 (MQ=255)
tGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCAtt > 1:699646/1‑68 (MQ=255)
tGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCAtt > 1:1615903/1‑68 (MQ=255)
tGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCAtt > 1:2812403/1‑68 (MQ=255)
tGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCAtt > 1:1318030/1‑68 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTc > 1:1917310/1‑68 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt > 1:3270785/1‑69 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt > 1:2880178/1‑69 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt > 1:514484/1‑69 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt > 1:2735602/1‑69 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt > 1:2623391/1‑69 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt < 1:2270715/69‑1 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt > 1:1216844/1‑69 (MQ=255)
aTCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt < 1:1036515/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCATTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:1344174/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:3332910/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:2817478/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:2600941/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:2178603/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:2163668/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:2345285/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:1496795/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:1229793/69‑1 (MQ=255)
cgcgCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:1369992/69‑1 (MQ=255)
gcgcTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTAc < 1:1314837/68‑1 (MQ=255)
ctggATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGt < 1:2660134/69‑1 (MQ=255)
ctggATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGt < 1:1487835/69‑1 (MQ=255)
gcAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCt < 1:243687/39‑1 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1345971/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:2682685/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1867251/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1473010/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:3003593/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:269810/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1248261/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1122053/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:586567/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1058068/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:769016/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:890565/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1676581/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:2352306/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:23473/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:1022544/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:2105398/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:2231406/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtcat > 1:2308198/1‑57 (MQ=255)
gcgcCTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGtca > 1:2574838/1‑56 (MQ=255)
ccTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCa < 1:2666770/69‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCa < 1:2359481/69‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCa < 1:2798465/69‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCa < 1:1623452/69‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTgg < 1:885504/68‑2 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:427719/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:1550025/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:572139/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:2146726/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:1064214/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:1873099/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:219470/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:2995286/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:1526441/68‑1 (MQ=255)
ccTGACGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:1553846/68‑1 (MQ=255)
tGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAgt < 1:2562223/69‑2 (MQ=255)
tGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAgg < 1:2316635/69‑1 (MQ=255)
gACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAgg < 1:165396/68‑1 (MQ=255)
aCGCCGCTCTGGCTTCCATCATTTCTACTATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGc < 1:847521/64‑1 (MQ=255)
ttCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAGGTATCGCACTGGc < 1:1563728/66‑1 (MQ=255)
ttCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAGGTATCGCACTGGc < 1:3113388/66‑1 (MQ=255)
ttCTATCATTTCTACCATTCTGGTTATCGCAGGGCATCAGAGCATTGGTGCAGGTATCGCACTGGc < 1:3066866/66‑1 (MQ=255)
|
CTGGAAATGATCGCGCTGGGCTGGATGAACATCGGTGCTGCAGTTGCGCCTGACGCCGCTCTGGCTTCTATCATTTCTACCATTCTGGTTATCGCAGGTCATCAGAGCATTGGTGCAGGTATCGCACTGGC > minE/1207163‑1207293
|
| 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
