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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
484,995 |
T→C |
73.4% |
S267S (AGT→AGC) |
tolB → |
periplasmic protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 484,995 | 0 | T | C | 73.4%
| 64.2
/ 17.7
| 56 | S267S (AGT→AGC) | tolB | periplasmic protein |
| Reads supporting (aligned to +/- strand): ref base T (2/13); new base C (24/17); total (26/30) |
| Fisher's exact test for biased strand distribution p-value = 2.93e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTGACTGATGGTCGCAGTAAC > minE/484952‑485061
|
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGaa > 1:1856121/1‑49 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGAtat > 1:1861295/1‑65 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:945185/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:1041975/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:2707384/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:264780/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:2975591/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:2435684/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:2994578/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:227312/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:3028843/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:1927284/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:3056005/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:1749366/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:3139484/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:3358478/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:55010/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:56290/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:608458/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:66874/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:125063/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:1231577/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTgg > 1:1192297/1‑69 (MQ=255)
cAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGCCTGAACCTGTACGTAATGGATTTg > 1:775160/1‑68 (MQ=255)
aGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGt < 1:3130148/57‑1 (MQ=255)
aGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGt < 1:2103283/57‑1 (MQ=255)
gcagcaAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:3306803/53‑1 (MQ=255)
gcagcaAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:839656/53‑1 (MQ=255)
gcagcaAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:2792293/53‑1 (MQ=255)
gcagcaAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:2484342/53‑1 (MQ=255)
gcagcaAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:2308949/53‑1 (MQ=255)
cagcaAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:1347919/52‑1 (MQ=255)
aaCTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGa < 1:556202/69‑1 (MQ=255)
aaCTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGa < 1:748076/69‑1 (MQ=255)
aaCTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGa < 1:1651093/69‑1 (MQ=255)
ggCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTa < 1:1523327/43‑1 (MQ=255)
gCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATcc > 1:3155755/1‑67 (MQ=255)
gCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATcc > 1:1556448/1‑67 (MQ=255)
ccGGTATCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:1617257/69‑1 (MQ=255)
ccGGTATCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:1613287/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:797311/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:801350/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:1215854/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:917244/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:1520764/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:1159640/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:471006/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:576519/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:160748/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:2814636/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:3130609/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:3083501/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:1916602/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:2217678/69‑1 (MQ=255)
ccGGTAGCCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTAACTGATGGTCGCa < 1:289092/69‑1 (MQ=255)
aGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTGACTGATGGTCGCAGTAAc < 1:1735310/69‑1 (MQ=255)
|
CAGACGGCAGCAAACTGGCATTCGCCTTGTCGAAAACCGGTAGTCTGAACCTGTACGTAATGGATTTGGCTTCTGGTCAGATCCGCCAGGTGACTGATGGTCGCAGTAAC > minE/484952‑485061
|
| 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
