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 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,764,664 |
T→C |
17.5% |
N106D (AAT→GAT) |
yidX ← |
predicted lipoproteinC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,764,664 | 0 | T | C | 17.5%
| 90.8
/ 14.4
| 40 | N106D (AAT→GAT) | yidX | predicted lipoproteinC |
| Reads supporting (aligned to +/- strand): ref base T (17/16); new base C (5/2); total (22/18) |
| Fisher's exact test for biased strand distribution p-value = 4.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01 |
CTTTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCT > W3110S.gb/3764596‑3764732
|
cTTTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTa < 1:4565128/71‑1 (MQ=255)
cTTTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTa < 1:3155580/71‑1 (MQ=255)
ttttCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTa > 1:4435404/1‑70 (MQ=255)
tttCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa > 1:968321/1‑70 (MQ=255)
ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaaaa > 1:4572567/1‑71 (MQ=255)
ttcttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa < 1:1384777/69‑1 (MQ=255)
ttcttcGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTaa < 1:4095727/66‑1 (MQ=255)
aTTCCAGTAGTAGTAAAGCGATATTGTGCCGTTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt > 1:3737383/1‑71 (MQ=255)
aTTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGt > 1:2430804/1‑71 (MQ=255)
cAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCa < 1:2565768/69‑1 (MQ=255)
cAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt < 1:1627600/70‑1 (MQ=255)
gtagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCg > 1:1704934/1‑67 (MQ=255)
gtagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCaa > 1:376341/1‑71 (MQ=255)
gtagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCa < 1:880440/70‑1 (MQ=255)
tagtaAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAAc < 1:3490427/71‑1 (MQ=255)
tatTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt > 1:466025/1‑53 (MQ=255)
tatTGTGCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTg > 1:861725/1‑47 (MQ=255)
ttGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtg < 1:3625399/68‑1 (MQ=255)
gtgCCGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGc > 1:289620/1‑44 (MQ=255)
ccGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt < 1:2097479/71‑1 (MQ=255)
cGGTAAATTTCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt > 1:2593697/1‑70 (MQ=255)
gTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATtg < 1:2162468/60‑1 (MQ=255)
gTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAg > 1:757849/1‑71 (MQ=255)
tAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGc < 1:4455326/62‑1 (MQ=255)
aTTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCa < 1:679519/38‑1 (MQ=255)
tttCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGc < 1:2934521/69‑1 (MQ=255)
tttCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTg > 1:4339932/1‑71 (MQ=255)
tttCTTTTTCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTg > 1:1227391/1‑71 (MQ=255)
cTTTTTCCCCGCATTTAAAACAAATCTTGCGTCAt > 1:687203/1‑35 (MQ=255)
tttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCAt > 1:389966/1‑71 (MQ=255)
ttCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCAtt > 1:3845455/1‑71 (MQ=255)
ttCCCCGCATCTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCAtt > 1:874395/1‑71 (MQ=255)
ccccGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCAtt > 1:3364468/1‑69 (MQ=255)
ccccGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTg < 1:2803473/70‑1 (MQ=255)
ccccGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTg < 1:307255/70‑1 (MQ=255)
gCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGtt < 1:1353640/50‑1 (MQ=255)
gCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTaa < 1:856213/52‑1 (MQ=255)
gCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCAt > 1:453883/1‑71 (MQ=255)
aTTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCt > 1:4406434/1‑71 (MQ=255)
aTTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCt > 1:3460480/1‑71 (MQ=255)
tttAAAACAAATCTTGCGTCATCGGCAACCTGAata < 1:4006709/36‑1 (MQ=255)
|
CTTTTCTTCTTCGTTATTCCAGTAGTAGTAAAGCGATATTGTGCCGGTAAATTTCTTTTTCCCCGCATTTAAAACAAATCTTGCGTCATCGGCAACCTGAATATTGTGCCGGTTAAGTGCTGGATCATTGAGCATCT > W3110S.gb/3764596‑3764732
|
| 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
