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 R1
|
311 |
50.1 |
4085234 |
95.9% |
3917739 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,538,437 |
G→A |
43.4% |
A170V (GCA→GTA) |
rhaS ← |
DNA‑binding transcriptional activator, L‑rhamnose‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,538,437 | 0 | G | A | 43.4%
| 40.2
/ 111.4
| 88 | A170V (GCA→GTA) | rhaS | DNA‑binding transcriptional activator, L‑rhamnose‑binding |
| Reads supporting (aligned to +/- strand): ref base G (22/27); new base A (24/14); total (47/41) |
| Fisher's exact test for biased strand distribution p-value = 1.29e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
GGCATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGATCTC > W3110S.gb/3538370‑3538507
|
ggCATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATacgc > 1:336263/1‑71 (MQ=255)
ccAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGtttt > 1:26651/1‑71 (MQ=255)
ccAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGtttt > 1:1841319/1‑71 (MQ=255)
ccAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGtttt > 1:2351775/1‑71 (MQ=255)
ccAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGtttt > 1:3911743/1‑71 (MQ=255)
acAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGtttt > 1:2884220/2‑71 (MQ=255)
aaTTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGtttt > 1:1087403/1‑69 (MQ=255)
aaTTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTcc < 1:838963/71‑1 (MQ=255)
aaTTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTcc < 1:566639/71‑1 (MQ=255)
aTTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTg < 1:2595310/64‑1 (MQ=255)
ttCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATacgc > 1:283156/1‑61 (MQ=255)
ttCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGtt > 1:1473396/1‑65 (MQ=255)
ttCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAg > 1:561673/1‑71 (MQ=255)
ttCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAg > 1:2595832/1‑71 (MQ=255)
cACCTGATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAgg > 1:3969264/1‑70 (MQ=255)
cACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAgg < 1:298084/70‑1 (MQ=255)
cACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAgg < 1:374112/70‑1 (MQ=255)
cACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAgg > 1:2532978/1‑70 (MQ=255)
cACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAgg > 1:1351469/1‑70 (MQ=255)
cACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGt > 1:3036268/1‑71 (MQ=255)
tCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTcc < 1:3958285/63‑1 (MQ=255)
tCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTtctc > 1:3022821/1‑71 (MQ=255)
tCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTtctc > 1:2334269/1‑71 (MQ=255)
tCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTtctc > 1:1926102/1‑71 (MQ=255)
ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGc > 1:1571543/1‑70 (MQ=255)
ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGc > 1:2081235/1‑70 (MQ=255)
ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCa < 1:330951/71‑1 (MQ=255)
ggCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCa < 1:2693776/71‑1 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCt < 1:2323396/48‑1 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCt < 1:2737406/48‑1 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCt < 1:3850816/48‑1 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCt < 1:864866/48‑1 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAAc > 1:2318099/1‑71 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAAc > 1:2844083/1‑71 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAAc > 1:1227183/1‑71 (MQ=255)
aaaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTACTGCAAAc > 1:3442021/1‑71 (MQ=255)
aaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTcc < 1:1842078/54‑1 (MQ=255)
aaaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATACGCt < 1:3888109/47‑1 (MQ=255)
aaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTg < 1:3777341/71‑1 (MQ=255)
aaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTg < 1:3022459/71‑1 (MQ=255)
aaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTg < 1:1321790/71‑1 (MQ=255)
aaTGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTg < 1:3437203/71‑1 (MQ=255)
tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATgc < 1:1320235/41‑1 (MQ=255)
tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTtctc < 1:3392274/59‑1 (MQ=255)
tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTtctc < 1:3049303/59‑1 (MQ=255)
tGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTtctc < 1:3468857/59‑1 (MQ=255)
gTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCttt < 1:1496187/71‑1 (MQ=255)
cctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAAc > 1:187764/1‑63 (MQ=255)
cctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAAc > 1:3359124/1‑63 (MQ=255)
cctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAAc > 1:1646108/1‑63 (MQ=255)
cctccAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCttt < 1:890879/69‑1 (MQ=255)
gccaggccagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgcag > 1:1578718/1‑70 (MQ=255)
gccaggccagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgcag > 1:424574/1‑70 (MQ=255)
gccaggccagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgcag > 1:3102441/1‑70 (MQ=255)
gccaggccagAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgcagc < 1:2886476/71‑1 (MQ=255)
cagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCaaa > 1:2576000/1‑49 (MQ=255)
cagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCaaa > 1:24039/1‑49 (MQ=255)
cagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCaaa > 1:1653770/1‑49 (MQ=255)
cagAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCaa > 1:2860938/1‑48 (MQ=255)
agAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGc < 1:3397290/52‑1 (MQ=255)
agAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAg > 1:977042/1‑71 (MQ=255)
gAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:2904075/71‑1 (MQ=255)
gAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:3693337/71‑1 (MQ=255)
gAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:831835/71‑1 (MQ=255)
gAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:3501896/71‑1 (MQ=255)
gAAGCAAGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:1990515/71‑1 (MQ=255)
aaGCATGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:2875221/70‑1 (MQ=255)
aaGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:2981360/70‑1 (MQ=255)
aaGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGt < 1:1074856/70‑1 (MQ=255)
aaGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTa < 1:3793186/71‑1 (MQ=255)
aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa > 1:1302018/1‑71 (MQ=255)
aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa > 1:4080167/1‑71 (MQ=255)
aGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa > 1:1633888/1‑71 (MQ=255)
gCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAAt > 1:2128743/1‑71 (MQ=255)
gCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAAt > 1:2014511/1‑71 (MQ=255)
aaGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgcagc < 1:3775881/57‑1 (MQ=255)
aaGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgcagc < 1:164813/57‑1 (MQ=255)
aaGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTg > 1:1249269/1‑71 (MQ=255)
aaGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGTGCAGTAATTg > 1:1433674/1‑71 (MQ=255)
aaGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTg > 1:3649247/1‑71 (MQ=255)
aaGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTg > 1:904882/1‑71 (MQ=255)
aaGTTGAGACGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTg > 1:1130790/1‑71 (MQ=255)
ttGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAag < 1:1293837/57‑1 (MQ=255)
tGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCAt > 1:3133697/1‑70 (MQ=255)
aCGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAAc > 1:1371059/1‑70 (MQ=255)
aCGTGATACGCTGTTTTCCAGGTTCTCCTGCAAACAGCTTTTACGCAGCAAGAGCAGt < 1:2884225/58‑1 (MQ=255)
gTGATTCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa > 1:3074611/1‑58 (MQ=255)
gTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTaa > 1:2857964/1‑58 (MQ=255)
tGATACGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGa < 1:2691685/71‑1 (MQ=255)
aTGTGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGAtc < 1:3830428/71‑1 (MQ=255)
tGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAg < 1:1335198/67‑1 (MQ=255)
gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgca > 1:414878/1‑40 (MQ=255)
gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgca > 1:2032642/1‑40 (MQ=255)
gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACgca > 1:1053124/1‑40 (MQ=255)
gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGAtctc > 1:593729/1‑71 (MQ=255)
gcgcTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGAtctc > 1:1534870/1‑71 (MQ=255)
|
GGCATCCCAATTCACCTCATCGGCAAAATGGTCCTCCAGCCAGGCCAGAAGCAAGTTGAGACGTGATGCGCTGTTTTCCAGGTTCTCCTGCAAACTGCTTTTACGCAGCAAGAGCAGTAATTGCATAAACAAGATCTC > W3110S.gb/3538370‑3538507
|
| 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
