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 |
|
A6 F28 I3 R2
|
24 |
47.7 |
2431847 |
96.1% |
2337004 |
60.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
894,732 |
C→T |
D445N (GAC→AAC) |
sapA ← |
predicted antimicrobial peptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 894,732 | 0 | C | T | 97.3%
| 112.3
/ ‑3.6
| 37 | D445N (GAC→AAC) | sapA | predicted antimicrobial peptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (23/13); total (24/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01 |
GTGGGCGAGGTTGGTCTGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTCCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATCCATCAA > minE/894670‑894792
|
gTGGGCGAGGTTGGTCTGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGt < 1:1823150/71‑1 (MQ=255)
gggCGAGGTTGGTCTGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTa > 1:101801/1‑71 (MQ=255)
cGAGGTTGGTCTGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTg > 1:770548/1‑71 (MQ=255)
cTGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGcc > 1:1633567/1‑70 (MQ=255)
tGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCggg > 1:2389458/1‑51 (MQ=255)
cGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAAc < 1:2017611/71‑1 (MQ=255)
gaatgaatTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTTCTGTCCGTCGCCCAAcc > 1:1355276/1‑71 (MQ=255)
gaatgaatTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAAcc > 1:891884/1‑71 (MQ=255)
gaatgaatTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAAc < 1:122722/70‑1 (MQ=255)
gaatTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTCCGGGTCGTTACTGTCCGTCGCCCAACCGGa > 1:1399273/1‑70 (MQ=255)
atTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATaa < 1:1688502/71‑1 (MQ=255)
ttGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAAc > 1:754014/1‑71 (MQ=255)
ccGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGt < 1:1371309/70‑1 (MQ=255)
ccGCGCAGCTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGt < 1:226344/70‑1 (MQ=255)
cTCAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAg < 1:875899/65‑1 (MQ=255)
cAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAAc > 1:439373/1‑58 (MQ=255)
cAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGAt > 1:1472812/1‑65 (MQ=255)
cAGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATgg > 1:1382149/1‑70 (MQ=255)
aGTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGc < 1:2407607/70‑1 (MQ=255)
gTAACGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATaa < 1:1785007/55‑1 (MQ=255)
aaCGGACGGAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACg > 1:1203708/1‑55 (MQ=255)
acggacggAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCa > 1:1080503/1‑43 (MQ=255)
acggacggAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCata > 1:2288645/1‑71 (MQ=255)
acggacggAAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCata > 1:52342/1‑71 (MQ=255)
gacggaAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCaa > 1:1667854/1‑41 (MQ=255)
acggaAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATCCa > 1:587848/1‑71 (MQ=255)
cggaAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATcc > 1:2344309/1‑69 (MQ=255)
cggaAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATcc > 1:74881/1‑69 (MQ=255)
cggaAGAAACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATcc > 1:1845819/1‑69 (MQ=255)
gaagaaACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATCCATCa < 1:575283/71‑1 (MQ=255)
gaagaaACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAAAGTCAGAt > 1:620631/1‑53 (MQ=39)
aagaaACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATcc > 1:1978932/1‑66 (MQ=255)
aagaaACTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATCCATCaa < 1:436536/71‑1 (MQ=255)
aaCTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGa > 1:1423574/1‑47 (MQ=255)
aaCTGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCt > 1:1324148/1‑55 (MQ=255)
tGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAAc < 1:2007258/38‑1 (MQ=255)
tGTTCGGGTCGTTACTGTCCGTCGCCCAACCGGATAAc < 1:741799/38‑1 (MQ=255)
|
GTGGGCGAGGTTGGTCTGCGAATGAATTGCCGCGCAGCTCAGTAACGGACGGAAGAAACTGTCCGGGTCGTTACTGTCCGTCGCCCAACCGGATAACGTCAGATCATGGCTCATATCCATCAA > minE/894670‑894792
|
| 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
