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 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,867,123 |
G→A |
100% |
P96L (CCG→CTG) |
nlpD ← |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,867,123 | 0 | G | A | 86.7%
| 75.5
/ 5.2
| 30 | P96L (CCG→CTG) | nlpD | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (0/4); new base A (9/17); total (9/21) |
| Fisher's exact test for biased strand distribution p-value = 2.87e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGC > W3110S.gb/2867057‑2867185
|
taACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgct < 1:2278885/70‑1 (MQ=255)
aCTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAgctgct > 1:2851720/1‑71 (MQ=255)
ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTTCTGAGc < 1:21/71‑1 (MQ=255)
ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:367008/71‑1 (MQ=255)
ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:1523277/71‑1 (MQ=255)
ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:1854352/71‑1 (MQ=255)
ccTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGc < 1:1922196/71‑1 (MQ=255)
tCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTa < 1:3273897/69‑1 (MQ=255)
aTGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCt > 1:286583/1‑70 (MQ=255)
aTGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg > 1:3657444/1‑71 (MQ=255)
aTGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg > 1:2144560/1‑71 (MQ=255)
tGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg < 1:1228742/70‑1 (MQ=255)
tGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg < 1:1110828/70‑1 (MQ=255)
tGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg < 1:1399625/70‑1 (MQ=255)
tGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGc < 1:3067206/71‑1 (MQ=255)
ttCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTg < 1:3500978/68‑1 (MQ=255)
ttCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCAc > 1:3383980/1‑71 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:1453701/1‑71 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:2312051/1‑71 (MQ=255)
cTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGa > 1:136761/1‑71 (MQ=255)
aCGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt < 1:217986/70‑1 (MQ=255)
aCGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt < 1:496992/70‑1 (MQ=255)
aCGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt < 1:1301153/70‑1 (MQ=255)
aCGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGAtt < 1:2773801/70‑1 (MQ=255)
gTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCt < 1:267891/46‑1 (MQ=255)
gTTATAGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCt < 1:2263502/46‑1 (MQ=255)
tataGACGATGCGTCCGTTTTCCATCTGTACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGgt > 1:16465/1‑71 (MQ=255)
tACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGgc < 1:3572998/67‑1 (MQ=255)
tACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGgc < 1:1254757/67‑1 (MQ=255)
tACCAGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGgc < 1:835612/67‑1 (MQ=255)
|
TAACTGCCTTTCGGAATGTTCCCATACTGACGGTTATAGACGATGCGTCCGTTTTCCATCTGTACCGGCTGCTGAGCTACTGGCTGCACTGGCTGGATTTGCGGTTGTTGAGTAGCCTGAATTTGTGGC > W3110S.gb/2867057‑2867185
|
| 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
