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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,045,839 |
T→A |
12.0% |
intergenic (+601/+194) |
yqiK → / ← rfaE |
conserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,045,839 | 0 | T | A | 12.0%
| 174.5
/ 13.4
| 66 | intergenic (+601/+194) | yqiK/rfaE | conserved hypothetical protein/fused heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (27/31); new base A (2/6); total (29/37) |
| Fisher's exact test for biased strand distribution p-value = 4.50e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGA > minE/2045771‑2045905
|
cgcTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat < 1:2460908/71‑1 (MQ=255)
cgcTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGta > 1:934496/1‑70 (MQ=255)
gcTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtata < 1:1240967/71‑1 (MQ=255)
gcTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtata < 1:893500/71‑1 (MQ=255)
tcatcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat < 1:3810546/68‑1 (MQ=255)
atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGta > 1:299217/1‑65 (MQ=255)
atcaACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAgg > 1:1848227/1‑70 (MQ=255)
caacaaTCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGa > 1:383422/1‑69 (MQ=255)
ggggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGtat < 1:379648/54‑1 (MQ=255)
ggggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTatgat < 1:2822319/71‑1 (MQ=255)
ggCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTAtgatga < 1:2250737/71‑1 (MQ=255)
gcaAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCt > 1:3826505/1‑71 (MQ=255)
caAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg > 1:1959571/1‑68 (MQ=255)
aaGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGaaa > 1:2838940/1‑53 (MQ=255)
aaGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCg > 1:1376259/1‑71 (MQ=255)
acgCTGAAACGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGt > 1:1708430/3‑70 (MQ=0)
ggCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGtcat < 1:1936945/71‑1 (MQ=255)
gCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTatgatg < 1:3100332/59‑1 (MQ=255)
tGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCg < 1:748236/64‑1 (MQ=255)
gAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAgg > 1:3395419/1‑47 (MQ=255)
aaaCGTGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTcatcat < 1:3550215/69‑1 (MQ=255)
aaaCGGGAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTAtgatga > 1:116466/1‑57 (MQ=0)
aaaCGGGAAAGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcat < 1:3128594/69‑1 (MQ=11)
aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGaaa < 1:2098056/44‑1 (MQ=255)
aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTat < 1:3155389/51‑1 (MQ=255)
aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTcatcat < 1:2923315/69‑1 (MQ=255)
aaaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATAc > 1:673150/1‑71 (MQ=255)
aaCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATAc < 1:2633942/70‑1 (MQ=255)
aCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTTTATAAg > 1:3420149/1‑38 (MQ=255)
aCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTc > 1:2261239/1‑59 (MQ=255)
aCGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTc > 1:3282549/1‑59 (MQ=255)
gggAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTgg < 1:3376571/71‑1 (MQ=11)
gggAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTATGATGAAGCACGTCATCATACTgg < 1:1049747/71‑1 (MQ=11)
ggAAAGCCTCTCCCGGAGAAGAGGGCTTTTAATAAGGAAAGGGTTa < 1:3541859/46‑1 (MQ=0)
gAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttg > 1:2125140/1‑71 (MQ=255)
aaaGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgt < 1:484967/71‑1 (MQ=255)
aGCCCCTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcatc < 1:1334196/61‑2 (MQ=9)
cccTCCCGAGGAAG‑GGGCCATAAATAAGGAAAGGGTCATGATGAAGCTACTcatcatcg < 1:994508/59‑3 (MQ=255)
cccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAg < 1:273649/46‑1 (MQ=255)
cccTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt < 1:3639705/71‑1 (MQ=255)
cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgt > 1:1881117/1‑66 (MQ=255)
cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa > 1:1424878/1‑71 (MQ=255)
cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa > 1:3654444/1‑71 (MQ=255)
cTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTa < 1:3464314/71‑1 (MQ=255)
cccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACt > 1:897779/1‑71 (MQ=255)
ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTatgat > 1:3361621/1‑37 (MQ=255)
ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGt > 1:11342/1‑46 (MQ=255)
ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGt > 1:1171079/1‑46 (MQ=255)
ccGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTg < 1:1935560/71‑1 (MQ=255)
cGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGt < 1:2794176/71‑1 (MQ=255)
gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTcatcat < 1:2934175/50‑1 (MQ=255)
gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTcatcat < 1:2451304/50‑1 (MQ=255)
gaagaaG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt < 1:321771/71‑1 (MQ=255)
aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt > 1:3731076/1‑70 (MQ=255)
aagaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt > 1:2619352/1‑70 (MQ=255)
agaag‑GGGCCTTGTATAAGGAAAGGTTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGt > 1:2305512/1‑68 (MQ=255)
gaag‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGtt < 1:1890929/68‑1 (MQ=255)
g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgt > 1:2122189/1‑55 (MQ=255)
g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgt > 1:2667839/1‑55 (MQ=255)
g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtg < 1:1989837/54‑1 (MQ=255)
g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtg < 1:3131370/54‑1 (MQ=255)
g‑gggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGttt < 1:881928/71‑1 (MQ=255)
ggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTgttgtt < 1:3154011/57‑1 (MQ=255)
ggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTgttgtt < 1:2941019/57‑1 (MQ=255)
ggCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTg < 1:3865645/61‑1 (MQ=255)
gCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTccc < 1:2440058/71‑1 (MQ=255)
ccTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTTCTGTTAAGTTTccc > 1:3193328/1‑70 (MQ=255)
ccTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCg < 1:2919349/71‑1 (MQ=255)
ccTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGATTccc > 1:595478/1‑70 (MQ=255)
cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGgttgtgttgt < 1:3029819/53‑1 (MQ=255)
cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa < 1:1786667/71‑1 (MQ=255)
cTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa > 1:1380385/1‑71 (MQ=255)
gTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGa < 1:1747711/68‑1 (MQ=255)
tataAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGtt < 1:1645400/61‑1 (MQ=255)
|
CGCTCATCAACAATCGGGGGGCAGCAAGGGGCTGAAACGGGAAAGCCCCTCCCGAAGAAG‑GGGCCTTGTATAAGGAAAGGGTTATGATGAAGCTCGTCATCATACTGGTTGTGTTGTTACTGTTAAGTTTCCCGA > minE/2045771‑2045905
|
| 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
