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 |
2,541,664 |
G→A |
78.9% |
E129K (GAA→AAA) |
crr → |
glucose‑specific enzyme IIA component of PTS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,541,664 | 0 | G | A | 78.9%
| 105.5
/ 25.7
| 52 | E129K (GAA→AAA) | crr | glucose‑specific enzyme IIA component of PTS |
| Reads supporting (aligned to +/- strand): ref base G (7/4); new base A (17/24); total (24/28) |
| Fisher's exact test for biased strand distribution p-value = 3.08e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
GAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAAC > W3110S.gb/2541604‑2541727
|
gaagaaGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAaga < 1:508485/65‑1 (MQ=255)
gaagaaGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAaga < 1:136354/65‑1 (MQ=255)
gaagaaGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAaga < 1:2875505/65‑1 (MQ=255)
gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc < 1:3121545/69‑1 (MQ=255)
agGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:413320/69‑1 (MQ=255)
agGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:3621395/69‑1 (MQ=255)
ggTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc < 1:2878731/66‑1 (MQ=255)
ggTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGACGCTGCTGAAAGAGAAAGcc < 1:2063668/66‑1 (MQ=255)
tCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTc < 1:2842360/69‑1 (MQ=255)
cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTc < 1:1351806/68‑1 (MQ=255)
cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCt > 1:1772115/1‑69 (MQ=255)
cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCt > 1:2499146/1‑69 (MQ=255)
cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCt > 1:2711790/1‑69 (MQ=255)
cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCt > 1:1870065/1‑69 (MQ=255)
cAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCt > 1:369735/1‑69 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTcga > 1:1617764/1‑67 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTcga > 1:1565460/1‑67 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTc > 1:1038566/1‑67 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa < 1:3026480/69‑1 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa < 1:1043523/69‑1 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa < 1:3550252/69‑1 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTa > 1:258470/1‑69 (MQ=255)
cgTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:1645119/60‑1 (MQ=255)
gAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGa > 1:957598/1‑68 (MQ=255)
ggCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCt > 1:1524679/1‑59 (MQ=255)
cGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:223448/48‑1 (MQ=255)
gATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt < 1:873017/68‑1 (MQ=255)
aTACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGTTTGTTa < 1:4739/69‑1 (MQ=255)
aTACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTa < 1:1884768/69‑1 (MQ=255)
aTACTGTCATTGAATTTGATCTGCCGCTGCTGAAaga > 1:499427/1‑37 (MQ=255)
aTACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt < 1:2728366/68‑1 (MQ=255)
gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc > 1:1725665/1‑39 (MQ=255)
gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc > 1:800541/1‑39 (MQ=255)
gTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGcc > 1:1357322/1‑39 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt > 1:2297315/1‑60 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgt > 1:2389860/1‑59 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTa > 1:2110532/1‑61 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTa > 1:2899560/1‑61 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTa > 1:2420245/1‑61 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTa > 1:3280080/1‑61 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGAAAGATAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa < 1:3187676/68‑1 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa > 1:717480/1‑38 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttgtt < 1:3605970/60‑1 (MQ=255)
gAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttg < 1:270122/55‑1 (MQ=255)
gAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttg < 1:899526/55‑1 (MQ=255)
gAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATg < 1:1133075/69‑1 (MQ=255)
tGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGa > 1:2607794/1‑69 (MQ=255)
cTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTAtc < 1:1869598/51‑1 (MQ=255)
cTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTAtc < 1:3173317/51‑1 (MQ=255)
gctgctGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCa < 1:2015329/65‑1 (MQ=255)
gctgctGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCa < 1:587157/65‑1 (MQ=255)
gctgAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAAc > 1:3670031/1‑68 (MQ=255)
|
GAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAAC > W3110S.gb/2541604‑2541727
|
| 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
