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 I2 R2
|
64 |
60.0 |
3197630 |
92.7% |
2964203 |
60.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
965,646 |
C→T |
G83D (GGC→GAC) |
ydeM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 965,646 | 0 | C | T | 98.4%
| 201.6
/ ‑6.6
| 63 | G83D (GGC→GAC) | ydeM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (30/31); minor base G (0/1); total (31/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGGCACACCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGCCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGTGGGTT > minE/965581‑965709
|
aGGCACACCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCa > 1:1425139/1‑71 (MQ=255)
aGGCACACCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCa < 1:2991025/71‑1 (MQ=255)
acacCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCa < 1:2803402/67‑1 (MQ=255)
acacCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGc > 1:988054/1‑71 (MQ=255)
acacCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGc > 1:2778223/1‑71 (MQ=255)
cattcattATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttg > 1:109254/1‑71 (MQ=255)
cattcattATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttg < 1:2141430/71‑1 (MQ=255)
cattcattATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttg < 1:2787718/71‑1 (MQ=255)
cattcattATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttg < 1:1462442/71‑1 (MQ=255)
cattATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGa > 1:217683/1‑71 (MQ=255)
attattCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGa > 1:371719/1‑70 (MQ=255)
attattCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGa < 1:2154191/70‑1 (MQ=255)
attattCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGa < 1:1639876/70‑1 (MQ=255)
attattCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGa > 1:33686/1‑70 (MQ=255)
ttattCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATa < 1:762436/71‑1 (MQ=255)
aaTAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTg < 1:805059/49‑1 (MQ=255)
tAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttgtt < 1:1462324/59‑1 (MQ=255)
tGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa > 1:514741/1‑71 (MQ=255)
tGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa > 1:1009040/1‑71 (MQ=255)
tGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa > 1:641241/1‑71 (MQ=255)
ccATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTg < 1:1275989/40‑1 (MQ=255)
ccATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTg < 1:2600468/40‑1 (MQ=255)
ccATTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAA‑AACTTTACg > 1:2602804/1‑70 (MQ=255)
aTTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCa > 1:2058378/1‑40 (MQ=255)
aTTCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCa > 1:2785602/1‑40 (MQ=255)
ttCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGc < 1:3157523/38‑1 (MQ=255)
ttCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGc < 1:1142826/38‑1 (MQ=255)
ttCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGc < 1:2635246/38‑1 (MQ=255)
ttCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACgg < 1:421201/69‑1 (MQ=255)
ttCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACgg < 1:3006700/69‑1 (MQ=255)
ttCGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGa > 1:752651/1‑70 (MQ=255)
cGTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGaaa < 1:3083230/70‑1 (MQ=255)
cGTTTGTAATGCATTAAAAATACGTTTTTGGGCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGaaa < 1:1013749/70‑1 (MQ=255)
gTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGaaaa < 1:1167064/70‑1 (MQ=255)
gTTTGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGaaaa < 1:427388/70‑1 (MQ=255)
tttGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa < 1:2634035/62‑1 (MQ=255)
tttGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa < 1:1600177/62‑1 (MQ=255)
tttGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa < 1:2920846/62‑1 (MQ=255)
tttGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa < 1:2530795/62‑1 (MQ=255)
ttGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAAt > 1:129250/1‑71 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttgt > 1:1106755/1‑42 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttgt > 1:2952037/1‑42 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttgt > 1:2445863/1‑42 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCgttgt > 1:23332/1‑42 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa > 1:2989655/1‑60 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa > 1:1953885/1‑60 (MQ=255)
tGTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTa > 1:1986945/1‑60 (MQ=255)
gTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAAt < 1:1569409/69‑1 (MQ=255)
gTAATGCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATc < 1:2290535/70‑1 (MQ=255)
gCATTAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGgc > 1:2330693/1‑70 (MQ=255)
ttAAAAATACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACgg > 1:564813/1‑54 (MQ=255)
ttAAAAATACGTTTTTGG‑‑TGCATAGCGTTGTTGATAGTGAATAACTTTACgg > 1:3058785/1‑52 (MQ=38)
aaaaTACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTAc > 1:507379/1‑49 (MQ=255)
aaaaTACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTAc > 1:523969/1‑49 (MQ=255)
aaaaTACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGccagccag < 1:195655/71‑1 (MQ=255)
aaaaTACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGccagccag < 1:64140/71‑1 (MQ=255)
aaaaTACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGccagccag < 1:2540185/71‑1 (MQ=255)
aaaTACGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGccagccag < 1:1962380/70‑1 (MQ=255)
aCGTTTTTGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGTgg > 1:692696/1‑71 (MQ=255)
tttttGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGTGGGtt > 1:958106/1‑71 (MQ=255)
tttttGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGTGGGtt < 1:229389/71‑1 (MQ=255)
ttttGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGTGGGtt > 1:2244026/1‑70 (MQ=255)
ttGGTCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGt > 1:466753/1‑63 (MQ=255)
|
AGGCACACCATTCATTATTCAATAAAATGCCATTCGTTTGTAATGCATTAAAAATACGTTTTTGGCCTGCATAGCGTTGTTGATAGTGAATAACTTTACGGAAAAAATCCAGGCCAGCCAGAGTGGGTT > minE/965581‑965709
|
| 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
