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 |
|
A5 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,524 |
T→G |
100% |
pseudogene (657/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,524 | 0 | T | G | 100.0%
| 239.8
/ NA
| 68 | pseudogene (657/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (31/37); total (31/37) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTA > W3110S.gb/3824456‑3824589
|
atcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGcgct < 1:863388/71‑1 (MQ=255)
tcatTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg > 1:449813/1‑71 (MQ=255)
catTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTgg > 1:13928/1‑71 (MQ=255)
atTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg > 1:4548516/1‑69 (MQ=255)
tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTg > 1:167669/1‑67 (MQ=255)
tGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGccc > 1:1538814/1‑71 (MQ=255)
gAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTtggccctggccc < 1:4046639/70‑1 (MQ=255)
aaGTGCTGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg < 1:2647979/70‑1 (MQ=255)
aGTGCAGGGGACGGCAGAAGGCGAGCCGTTAACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g > 1:2886364/1‑71 (MQ=255)
gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gg < 1:923932/71‑1 (MQ=255)
gTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gg < 1:1994542/71‑1 (MQ=255)
gCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg > 1:1480887/1‑71 (MQ=255)
aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggga < 1:1522694/71‑3 (MQ=255)
aGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggga < 1:4378484/71‑3 (MQ=255)
ggggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g < 1:4226278/65‑1 (MQ=255)
ggggACGGCAGAAGGCGAGCCGTTAACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggggaa < 1:3837257/71‑4 (MQ=255)
gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggtga < 1:2598685/69‑4 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa < 1:1499694/61‑1 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg < 1:2910146/71‑1 (MQ=255)
cGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa > 1:3978112/1‑71 (MQ=255)
cGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa < 1:4209245/71‑1 (MQ=255)
cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGc > 1:339659/1‑52 (MQ=255)
aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:1606050/70‑1 (MQ=255)
gAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAt > 1:2522061/1‑71 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt > 1:1012633/1‑71 (MQ=255)
cGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggg > 1:2554024/1‑52 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg < 1:3843503/46‑1 (MQ=255)
aGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc < 1:689904/70‑1 (MQ=255)
ccGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCg < 1:3549784/44‑1 (MQ=38)
cGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:1045066/59‑1 (MQ=255)
gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGa > 1:827105/1‑43 (MQ=38)
gTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGc < 1:85134/71‑1 (MQ=255)
ttCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCa < 1:2191066/71‑1 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg > 1:3637988/1‑70 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:550185/70‑1 (MQ=255)
aCCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAAGCGAATCCATTGTAGCGACGCAGaa < 1:2276915/71‑1 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:4215171/67‑1 (MQ=255)
ccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAgg > 1:1521965/1‑71 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga > 1:275696/1‑47 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑g > 1:4060126/1‑37 (MQ=38)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga > 1:640054/1‑46 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGt < 1:4021393/55‑1 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGt < 1:3244514/55‑1 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcg > 1:412064/1‑71 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa > 1:2041695/1‑59 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa > 1:4157536/1‑59 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc < 1:1080183/69‑1 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggg < 1:3134011/39‑2 (MQ=37)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCg < 1:2722991/57‑1 (MQ=255)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:948776/65‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGCATCCATTGTAGCGACGCAGAAGgcggcg > 1:94244/1‑71 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCg < 1:2717821/56‑1 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa > 1:3403402/1‑57 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg < 1:1012166/71‑1 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa < 1:2067287/43‑1 (MQ=25)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcggc > 1:3883829/1‑69 (MQ=255)
gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt > 1:3530465/1‑71 (MQ=255)
gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt < 1:1254803/71‑1 (MQ=255)
agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCt > 1:733407/1‑70 (MQ=255)
aCTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa > 1:2816843/1‑70 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCa < 1:3865904/69‑1 (MQ=255)
tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc < 1:1259767/46‑1 (MQ=255)
tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaaa > 1:3890538/1‑70 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:997221/3‑70 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACCCAGAAGGCGGCGCTGGCAAACt < 1:766962/68‑1 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCg > 1:3699835/1‑41 (MQ=255)
gttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt > 1:1406739/1‑68 (MQ=255)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:169110/45‑1 (MQ=255)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAttttt < 1:1072893/71‑1 (MQ=255)
ggCGCTGGCCCGAGGGGGAATCGAATCGATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:1647864/70‑1 (MQ=255)
|
ATCATTGAAGTGCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTA > W3110S.gb/3824456‑3824589
|
| 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
