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 F3 I0 R2
|
52 |
68.8 |
5189613 |
98.4% |
5106579 |
62.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,533:1 |
+G |
100% |
pseudogene (666/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,533 | 1 | . | G | 100.0%
| 187.8
/ NA
| 53 | pseudogene (666/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (22/31); total (22/31) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch. |
GCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > W3110S.gb/3824467‑3824597
|
gCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg > 1:4622212/1‑71 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg > 1:3305026/1‑70 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:2559829/70‑1 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:2631034/70‑1 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:1734948/70‑1 (MQ=255)
cAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:3109300/70‑1 (MQ=255)
gggACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGACCGA‑gggggaa > 1:3599581/1‑67 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg < 1:1557950/71‑1 (MQ=255)
gACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggg < 1:299834/64‑1 (MQ=255)
aCGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcga < 1:3871590/71‑1 (MQ=255)
cGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:1807758/63‑1 (MQ=255)
cAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATcc < 1:411236/71‑1 (MQ=255)
aGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCa < 1:2246513/71‑1 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCAtt > 1:1719010/1‑71 (MQ=255)
aaGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg > 1:2894228/1‑57 (MQ=255)
aGGCGAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg < 1:4632748/71‑1 (MQ=255)
gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTg < 1:4486315/67‑1 (MQ=255)
gAGCCGTTCACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTa > 1:4043597/1‑69 (MQ=255)
gTTCACACATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACg > 1:668943/1‑70 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat > 1:163769/1‑53 (MQ=255)
cACCCATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg > 1:3640694/1‑70 (MQ=255)
cccATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAg > 1:176646/1‑71 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcg < 1:3332186/46‑1 (MQ=255)
cATGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggc < 1:369018/71‑1 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaat < 1:1469018/48‑1 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGc > 1:197602/1‑63 (MQ=255)
aTGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcg < 1:1850322/71‑1 (MQ=255)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑ggggg > 1:2176843/1‑38 (MQ=37)
tGAAGAGCTACTCACCTTGTTGGCGCTGGCCCGA‑gggg < 1:5143487/38‑1 (MQ=38)
gAAGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGgaatcgaa > 1:2672562/1‑45 (MQ=255)
aaGAGCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGgcggcg < 1:2654322/71‑1 (MQ=255)
agagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGgcgc < 1:1267080/71‑1 (MQ=255)
gagCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:3357141/60‑1 (MQ=255)
agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGaa < 1:469377/61‑1 (MQ=255)
agCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTg > 1:4600752/1‑71 (MQ=255)
gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTgg > 1:2565127/1‑71 (MQ=255)
gCTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTg < 1:1739820/70‑1 (MQ=255)
cTACTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGc < 1:539001/50‑1 (MQ=255)
cTCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCaa < 1:3375744/70‑1 (MQ=255)
tCACCTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa > 1:2412801/1‑48 (MQ=255)
caccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACt > 1:790400/4‑71 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGGAAACTg < 1:10642/69‑1 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTg < 1:2769712/69‑1 (MQ=255)
accTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTg < 1:3509588/69‑1 (MQ=255)
ccTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGa < 1:2986389/70‑1 (MQ=255)
cTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt < 1:780935/71‑1 (MQ=255)
cTTGTTGGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAt < 1:31328/71‑1 (MQ=255)
ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGa > 1:4222649/1‑43 (MQ=37)
ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:439361/1‑71 (MQ=255)
ttgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:5059793/1‑71 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:4863042/1‑70 (MQ=255)
tgttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtt > 1:1389476/1‑70 (MQ=255)
gttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGAtttt > 1:4115959/1‑71 (MQ=255)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAg < 1:948076/45‑1 (MQ=255)
ttgGCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAggcgg > 1:4122365/1‑52 (MQ=255)
ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:2264267/70‑1 (MQ=255)
ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:532245/70‑1 (MQ=255)
ggCGCTGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:4133903/70‑1 (MQ=255)
gcgctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTaa < 1:2399600/67‑1 (MQ=255)
gcgctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:3301029/66‑1 (MQ=255)
ctGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTaa > 1:4779285/1‑67 (MQ=255)
tGGCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTa < 1:3004183/65‑1 (MQ=255)
ggCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGa < 1:4901872/38‑1 (MQ=38)
ggCCCGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGAc > 1:542586/1‑71 (MQ=255)
cccGAGGGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACt > 1:1483328/1‑70 (MQ=255)
|
GCAGGGGACGGCAGAAGGCGAGCCGTTCACCCATGAAGAGCTACTCATCTTGTTGGCTCTGGCCCGA‑GGGGAATCGAATCCATTGTAGCGACGCAGAAGGCGGCGCTGGCAAACTGATTTTTAAGGCGACT > W3110S.gb/3824467‑3824597
|
| 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
