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 |
626,032 |
T→C |
55.8% |
L323S (TTG→TCG) |
lpxK → |
lipid A 4'kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 626,032 | 0 | T | C | 55.8%
| 10.6
/ 38.2
| 52 | L323S (TTG→TCG) | lpxK | lipid A 4'kinase |
| Reads supporting (aligned to +/- strand): ref base T (6/17); new base C (9/20); total (15/37) |
| Fisher's exact test for biased strand distribution p-value = 7.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
ATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGC > minE/625969‑626100
|
aTTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTgg < 1:1851114/69‑1 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:1079344/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:827111/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:3298244/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:2794573/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:2577071/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:2361441/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:1719477/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:1591857/1‑69 (MQ=255)
tGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCtt > 1:1583409/1‑69 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:3176427/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:2588604/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:2622608/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:2676104/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:2421481/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:1556243/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:2701329/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:29886/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:3077884/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:3133223/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:314524/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:1888115/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:112947/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:3380561/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:1661076/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:1070086/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:378533/69‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACt < 1:63476/68‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACt < 1:359646/68‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACt < 1:1595054/68‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACt < 1:1622405/68‑1 (MQ=255)
cGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACt < 1:2280595/68‑1 (MQ=255)
gCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:892930/68‑1 (MQ=255)
aaCCAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:3318673/49‑1 (MQ=255)
ccAGCGAAACTGCTTGCGCAACTAACCTCGCTGGCTTCTGGCCACTa < 1:2151610/47‑1 (MQ=255)
gtaaCTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGAt < 1:180802/67‑1 (MQ=255)
gAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGAt < 1:2358876/69‑1 (MQ=255)
gAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGAt < 1:1227731/69‑1 (MQ=255)
gAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGAt < 1:1887778/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:1593228/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:1911507/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:2264693/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:2995774/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:2327119/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:2906607/69‑1 (MQ=255)
tACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATg < 1:1139540/69‑1 (MQ=255)
aaCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGc > 1:3294364/1‑68 (MQ=255)
aaCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt > 1:938306/1‑69 (MQ=255)
aaCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt > 1:666254/1‑69 (MQ=255)
aaCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt > 1:3389577/1‑69 (MQ=255)
aaCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt > 1:2507615/1‑69 (MQ=255)
aaCCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCt > 1:1612145/1‑69 (MQ=255)
tGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGc > 1:397555/1‑69 (MQ=255)
|
ATTTGCCTGTAGACGCACAGCTTTCAGGTGATGAACCAGCGAAACTGCTTACGCAACTAACCTTGCTGGCTTCTGGCAACTAGTTACGCCGCGGCAGCGTTCGATTGATGGAGTCATGAATGTCGCTGCCGC > minE/625969‑626100
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
