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 |
1,303,633 |
G→T |
100% |
Q246Y (CAG→TAT) |
oppA → |
oligopeptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,303,633 | 0 | G | T | 100.0%
| 145.3
/ NA
| 50 | Q246Y (CAG→TAT) | oppA | oligopeptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (20/30); total (20/30) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAATC > W3110S.gb/1303566‑1303696
|
tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa < 1:3441375/71‑1 (MQ=255)
tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa < 1:1918543/71‑1 (MQ=255)
tAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa < 1:1913936/71‑1 (MQ=255)
gaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa < 1:249080/71‑1 (MQ=255)
gaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa < 1:2146871/71‑1 (MQ=255)
gaacgaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTa < 1:3111321/71‑1 (MQ=255)
gaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTa < 1:860883/62‑1 (MQ=255)
gaaTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTg > 1:2208225/1‑71 (MQ=255)
gaaTCGTTCATGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTg > 1:3730641/1‑71 (MQ=255)
aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc < 1:2907703/71‑1 (MQ=255)
aTCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGcc < 1:1752764/71‑1 (MQ=255)
gTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTAt > 1:675062/1‑71 (MQ=255)
cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt > 1:3041864/1‑61 (MQ=255)
cTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt > 1:1214677/1‑61 (MQ=255)
aCGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTg < 1:2644929/71‑1 (MQ=255)
cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:732601/71‑1 (MQ=255)
cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:2331447/71‑1 (MQ=255)
cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:1169042/71‑1 (MQ=255)
cGACCTACTGGAACAACGCGAAAACCGTTATTAACTATGAAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:1247352/71‑1 (MQ=255)
aCCTACTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa < 1:947748/71‑1 (MQ=255)
aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt > 1:2055262/1‑68 (MQ=255)
aCTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGAt > 1:3982245/1‑68 (MQ=255)
aCTGGAACAACGCGAAAACCGTTATTAACTATGTAAACTATTTGCCTATTGCTTCTGAAGTTACCGATGt > 1:884637/1‑70 (MQ=255)
cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTAtt > 1:2139246/1‑41 (MQ=38)
cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc > 1:3227605/1‑70 (MQ=255)
cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc > 1:3619537/1‑70 (MQ=255)
cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc < 1:3236235/70‑1 (MQ=255)
cTGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTc > 1:1298878/1‑70 (MQ=255)
tGGAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa < 1:434899/65‑1 (MQ=255)
ggAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAAc > 1:1185987/1‑71 (MQ=255)
gAACAACGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATg > 1:1235680/1‑65 (MQ=255)
acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:3920445/56‑1 (MQ=255)
acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:3804533/56‑1 (MQ=255)
acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:3880788/56‑1 (MQ=255)
acGCGAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTAc > 1:3180559/1‑71 (MQ=255)
cgAAAACCGTTATTAACTATGTCACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt < 1:611686/71‑1 (MQ=255)
cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt < 1:4056358/71‑1 (MQ=255)
cgAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt < 1:1348854/71‑1 (MQ=255)
gAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:1093843/52‑1 (MQ=255)
gAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:3671376/52‑1 (MQ=255)
gAAAACCGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTAcc < 1:1715165/52‑1 (MQ=255)
aaCCGTTATTAACTATTTAACCTATTTGCCTATTGCTTCTGAAGTTACCGa < 1:3698828/51‑1 (MQ=255)
cGTTATTAACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAgtggt > 1:2334292/1‑70 (MQ=255)
ttattaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGt < 1:3016351/62‑1 (MQ=255)
attaACTATGTAACCTATTTGCCTATTGCTTCTGAAg > 1:1450489/1‑37 (MQ=37)
attaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTa > 1:3081539/1‑40 (MQ=38)
attaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAAt > 1:1727962/1‑71 (MQ=255)
attaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAAt > 1:893096/1‑71 (MQ=255)
ttaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCg < 1:3237599/42‑1 (MQ=38)
ttaACTATGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAATc < 1:3121996/71‑1 (MQ=255)
|
TAAACGAACGAATCGTTCTTGAACGCAGCCCGACCTACTGGAACAACGCGAAAACCGTTATTAACCAGGTAACCTATTTGCCTATTGCTTCTGAAGTTACCGATGTCAACCGCTACCGTAGTGGTGAAATC > W3110S.gb/1303566‑1303696
|
| 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
