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 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
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%
| 156.0
/ NA
| 54 | 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 (28/26); total (28/26) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTA > W3110S.gb/2866046‑2866176
|
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta < 1:4386990/71‑1 (MQ=255)
cacacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:3727517/1‑71 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:3150776/1‑71 (MQ=255)
cacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:148773/71‑1 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1374172/60‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:2629769/68‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc < 1:3219777/71‑1 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:3351216/55‑1 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:4218476/54‑1 (MQ=255)
tGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa > 1:1185318/1‑70 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:3468156/1‑49 (MQ=255)
gCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa > 1:3253846/1‑70 (MQ=255)
gCGATAACAGTTCCTCGTCGGCCAAATCGTTATCACTAGGTTCCAATTc > 1:4034559/1‑49 (MQ=255)
aTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAAcc > 1:2089359/1‑71 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:2917717/49‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:3390754/70‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:3394268/70‑1 (MQ=255)
gTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc < 1:3976268/58‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg < 1:2882982/46‑1 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCa < 1:1735439/58‑1 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTTCTAAGGCCTTTTCGTCAAAAACCTCaa > 1:328929/1‑66 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:1191654/1‑43 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:588506/1‑52 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTc > 1:2550076/1‑52 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCg < 1:4335350/70‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:3818000/35‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:1295438/35‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:2661158/1‑70 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:4355800/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:1063110/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:3265572/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:1397964/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:1988448/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:2097882/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTcta > 1:2300062/1‑35 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:521559/1‑56 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGtt < 1:2212885/69‑1 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:739225/1‑71 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:762110/1‑71 (MQ=255)
ggCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtca < 1:79084/70‑1 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa < 1:3737492/46‑1 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCaaa < 1:514463/71‑1 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCttt > 1:2201992/1‑38 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt > 1:4577305/1‑37 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTc > 1:3333592/1‑41 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg < 1:2699986/71‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAATCCg < 1:603880/71‑1 (MQ=255)
aTCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCa < 1:2381811/70‑1 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATc < 1:1318436/71‑1 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:990097/1‑53 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCtt < 1:999380/71‑1 (MQ=255)
aCTGGGTTCAAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtct > 1:3849279/1‑53 (MQ=255)
gggTTCCAATTCTACTAAGTCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAt > 1:2759216/1‑71 (MQ=255)
ttCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTa < 1:1184674/71‑1 (MQ=255)
|
CACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTA > W3110S.gb/2866046‑2866176
|
| 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
