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 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
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%
| 207.0
/ NA
| 68 | 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 (33/35); total (33/35) |
| 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
|
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:373078/1‑71 (MQ=255)
cAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAAtt > 1:3035283/1‑71 (MQ=255)
aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:4333817/71‑1 (MQ=255)
aaCACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:3907622/71‑1 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:1708262/1‑71 (MQ=255)
acacGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctac > 1:2103673/1‑71 (MQ=255)
acGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctacta < 1:4602595/71‑1 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt > 1:3191562/1‑71 (MQ=255)
tgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCt < 1:2848520/71‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt < 1:5054633/70‑1 (MQ=255)
gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtttt < 1:3051732/70‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:4598409/51‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:3679487/51‑1 (MQ=255)
cTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaa < 1:969795/71‑1 (MQ=255)
cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa < 1:5087198/70‑1 (MQ=255)
tAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCt > 1:193237/1‑71 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:3844100/47‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa < 1:2862782/49‑1 (MQ=255)
aCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:3825429/70‑1 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:4579653/1‑47 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAgg > 1:3727864/1‑49 (MQ=255)
aGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAgg > 1:4721558/1‑49 (MQ=255)
ttCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:1000098/60‑1 (MQ=255)
tCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTcc > 1:3841060/1‑71 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:1642359/1‑37 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTc > 1:2392161/1‑37 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:1728755/1‑43 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:875240/1‑43 (MQ=255)
ccTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTaa > 1:1814880/1‑43 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:4616516/1‑71 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt < 1:5084403/71‑1 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt < 1:629687/71‑1 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:2346666/1‑71 (MQ=255)
ctctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGt > 1:2575720/1‑71 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTctact < 1:4608518/39‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTcta < 1:4747634/37‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTc < 1:915760/35‑1 (MQ=255)
tctTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCtt < 1:3461368/47‑1 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTctac < 1:4621661/36‑1 (MQ=255)
ttCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:2721477/1‑56 (MQ=255)
tCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAg > 1:1075466/1‑39 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTctacta > 1:3371108/1‑36 (MQ=255)
cGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtctc > 1:4943961/1‑70 (MQ=255)
gCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatc < 1:2152242/71‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:4097911/71‑1 (MQ=255)
ccAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca < 1:583993/71‑1 (MQ=255)
aaaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:4206747/47‑1 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTc < 1:5100657/52‑1 (MQ=255)
aaTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAt < 1:530360/71‑1 (MQ=255)
aTCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaa > 1:147212/1‑46 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc > 1:4437614/1‑71 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc > 1:2542092/1‑71 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc > 1:495850/1‑71 (MQ=255)
tCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc > 1:1897064/1‑71 (MQ=255)
cGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCaa < 1:569208/51‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:2252728/1‑44 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaaaa > 1:3627441/1‑44 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTcc < 1:2075914/70‑1 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg > 1:281332/1‑71 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg > 1:4322906/1‑71 (MQ=255)
gTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCg > 1:3053233/1‑71 (MQ=255)
ttATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGc < 1:5146787/71‑1 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:2989595/38‑1 (MQ=255)
tCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCaaa < 1:1668494/38‑1 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCtt < 1:4265999/71‑1 (MQ=255)
aCTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCtt < 1:2370144/71‑1 (MQ=255)
gggTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAt > 1:1811865/1‑71 (MQ=255)
ttCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTa < 1:5105317/71‑1 (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
