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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,541,664 |
G→A |
87.2% |
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 | 87.2%
| 98.1
/ 7.6
| 39 | E129K (GAA→AAA) | crr | glucose‑specific enzyme IIA component of PTS |
| Reads supporting (aligned to +/- strand): ref base G (3/2); new base A (16/18); total (19/20) |
| Fisher's exact test for biased strand distribution p-value = 6.61e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01 |
GCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAACTGATCAA > W3110S.gb/2541601‑2541734
|
gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAgaga > 1:2351344/1‑70 (MQ=255)
gCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAgaga > 1:1342905/1‑70 (MQ=255)
gaagaaGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATATGCCGCTGCTGAAAGAGAAAGc > 1:3604627/1‑71 (MQ=255)
gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCaa < 1:2694718/71‑1 (MQ=255)
gaagGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:2094142/71‑1 (MQ=255)
aGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTAc < 1:2689690/70‑1 (MQ=255)
tGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAagag < 1:3440239/50‑1 (MQ=255)
tGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAagag < 1:2286168/50‑1 (MQ=255)
tGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAagag < 1:866257/50‑1 (MQ=255)
tGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAagag < 1:133766/50‑1 (MQ=255)
aaaGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGaa > 1:2343585/1‑50 (MQ=255)
aGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTAcc < 1:1628762/61‑1 (MQ=255)
ttGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCt > 1:2554567/1‑61 (MQ=255)
ttGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCt > 1:1287529/1‑61 (MQ=255)
tGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttg > 1:3126045/1‑71 (MQ=255)
tGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGgttg > 1:2132092/1‑71 (MQ=255)
cTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:152382/43‑1 (MQ=255)
cTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:1679477/43‑1 (MQ=255)
cTGTCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:2548204/43‑1 (MQ=255)
tCATTGAATTTGATCTGCCGCTGCTTAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa > 1:1126421/1‑70 (MQ=255)
tCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCaa > 1:3048245/1‑70 (MQ=255)
tCATTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCAGGTTGTTATCTCCaa > 1:683352/1‑70 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACAt > 1:1936891/1‑71 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGt > 1:1036352/1‑40 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAAc < 1:951488/69‑1 (MQ=255)
aTTGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACAt > 1:1195377/1‑71 (MQ=255)
ttGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:1082977/37‑1 (MQ=255)
ttGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:2907269/37‑1 (MQ=255)
ttGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:1638817/37‑1 (MQ=255)
ttGAATTTGATCTGCC‑CTGCTGAAAGAGAAAGCCaa < 1:277819/36‑1 (MQ=21)
tGAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCaa < 1:2860882/36‑1 (MQ=255)
gAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTAt > 1:640776/1‑59 (MQ=255)
gAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGa > 1:1860176/1‑71 (MQ=255)
gAATTTGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGa > 1:1460313/1‑71 (MQ=255)
tttGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGa < 1:2798876/71‑1 (MQ=255)
tGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGaaa > 1:3193089/1‑71 (MQ=255)
tGATCTGCCGCTGCTGAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGaaa > 1:3010914/1‑71 (MQ=255)
ctgAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAACTg < 1:769015/69‑1 (MQ=255)
ctgAAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACAAAATCAAAGAACTg < 1:265160/69‑1 (MQ=255)
gAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAACTGATCaa < 1:3629418/71‑1 (MQ=255)
gAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAACTGATCaa < 1:405355/71‑1 (MQ=255)
gAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAACTGATCaa < 1:2246621/71‑1 (MQ=255)
|
GCTGAAGAAGGTCAGCGCGTGAAAGTTGGCGATACTGTCATTGAATTTGATCTGCCGCTGCTGGAAGAGAAAGCCAAGTCTACCCTGACTCCGGTTGTTATCTCCAACATGGACGAAATCAAAGAACTGATCAA > W3110S.gb/2541601‑2541734
|
| 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
