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 |
2,866,110 |
T→A |
100% |
intergenic (‑20/+160) |
rpoS ← / ← nlpD |
RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,866,110 | 0 | T | A | 100.0%
| 197.9
/ NA
| 66 | intergenic (‑20/+160) | rpoS/nlpD | RNA polymerase, sigma S (sigma 38) factor/predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (33/33); total (33/33) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTA > W3110S.gb/2866043‑2866176
|
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt < 1:2373986/70‑1 (MQ=255)
acacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTct < 1:1530183/71‑1 (MQ=255)
acacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:1244990/1‑70 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAt > 1:608940/1‑67 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac < 1:3887792/71‑1 (MQ=255)
acacGCTGTGTGGCT‑CCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3299158/71‑1 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:4655453/71‑1 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:4186087/71‑1 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:1057985/71‑1 (MQ=255)
cTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:105303/1‑65 (MQ=255)
tgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:3514968/71‑1 (MQ=255)
ggCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt > 1:4055716/1‑70 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAgg > 1:3600261/1‑64 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc < 1:2072738/71‑1 (MQ=255)
cccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:3273327/58‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:4310691/64‑1 (MQ=255)
ccTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGt < 1:742014/69‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:4445987/1‑51 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:3789466/1‑51 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:234009/54‑1 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:182189/1‑54 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:4401125/1‑70 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:370067/1‑70 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:5137638/1‑70 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:4451838/70‑1 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:4995942/70‑1 (MQ=255)
gATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:855669/68‑1 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:618686/1‑52 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:3050407/1‑69 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc > 1:1961809/1‑62 (MQ=255)
aaCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc > 1:1955565/1‑62 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:4778846/65‑1 (MQ=255)
cAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa > 1:2257125/1‑71 (MQ=255)
gTTCCTCTTCGGCCAAATCGTTATCACTTGGTTCCAATTCTACTAAGGCCTTTTCGt < 1:2799923/57‑1 (MQ=255)
gTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCa < 1:4903389/59‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc < 1:4742054/71‑1 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAAATCTACTAAGGCCTTTTCGTc > 1:1945442/1‑55 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:5127015/40‑1 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg < 1:1060224/70‑1 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:1465556/1‑71 (MQ=255)
ctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:3027047/1‑55 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:3477267/1‑38 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAc > 1:227554/1‑57 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatc > 1:4838511/1‑70 (MQ=255)
cAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaa < 1:136994/71‑1 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt > 1:3845409/1‑40 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa > 1:1044275/1‑48 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatc > 1:4601956/1‑68 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaaa < 1:3147155/71‑1 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt < 1:1703949/38‑1 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAt > 1:322096/1‑71 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt < 1:3831552/71‑1 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt > 1:5154499/1‑71 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt > 1:457161/1‑71 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt > 1:4079296/1‑37 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc < 1:3092416/70‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc < 1:2063246/70‑1 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCAt < 1:1796674/70‑1 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCtt > 1:268865/1‑71 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCt < 1:4591140/70‑1 (MQ=255)
cTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGATCTCATCAAATTCCGCATCTTc < 1:3334066/71‑1 (MQ=255)
tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTc > 1:3748043/1‑45 (MQ=255)
tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc > 1:3080254/1‑62 (MQ=255)
tGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTc < 1:1189534/70‑1 (MQ=255)
ggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCC‑CATCTTCAtt > 1:1956875/1‑70 (MQ=255)
ttCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTa < 1:2996157/71‑1 (MQ=255)
|
CAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTA > W3110S.gb/2866043‑2866176
|
| 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
