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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,823,628 |
G→A |
63.8% |
intergenic (+373/+585) |
nrfG → / ← pheU |
heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,823,628 | 0 | G | A | 63.8%
| 57.8
/ 62.6
| 69 | intergenic (+373/+585) | nrfG/pheU | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
| Reads supporting (aligned to +/- strand): ref base G (12/13); new base A (21/23); total (33/36) |
| 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 |
CGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATG > minE/2823573‑2823694
|
cgcTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCcaca < 1:2655658/71‑1 (MQ=255)
aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCgatga < 1:2810229/54‑1 (MQ=255)
aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt < 1:52914/71‑1 (MQ=255)
aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt < 1:4833029/71‑1 (MQ=255)
aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt < 1:5120561/71‑1 (MQ=255)
ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtt < 1:2710898/71‑1 (MQ=255)
ttGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAt > 1:5096634/1‑70 (MQ=255)
gAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCga > 1:68539/1‑48 (MQ=255)
gAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCg > 1:3857910/1‑47 (MQ=255)
gAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATa > 1:4500979/1‑53 (MQ=255)
ggAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTa < 1:3574360/71‑1 (MQ=255)
ggAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTa < 1:2707269/71‑1 (MQ=255)
gcatAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAAt > 1:3131411/2‑44 (MQ=255)
gcatAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCta > 1:3974930/2‑69 (MQ=255)
catAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCtata < 1:743277/70‑1 (MQ=255)
catAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAg < 1:244275/71‑1 (MQ=255)
ataataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGa < 1:4371500/71‑1 (MQ=255)
aataGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTAtttt > 1:4744411/1‑56 (MQ=255)
ataGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATgg > 1:579609/1‑71 (MQ=255)
ataGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATg < 1:4250364/70‑1 (MQ=255)
taGAAACTCATTCGAAAAGGGAATGATGCAATGATa < 1:1510880/36‑1 (MQ=255)
gAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGa > 1:119876/1‑65 (MQ=255)
gAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt > 1:5638761/1‑71 (MQ=255)
aaCTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGa < 1:2300128/63‑1 (MQ=255)
aaCTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttta < 1:5437722/71‑1 (MQ=255)
aCTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttat > 1:257954/1‑71 (MQ=255)
cTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAttttt < 1:110126/49‑1 (MQ=255)
cTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATg > 1:4165870/1‑63 (MQ=255)
tCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGa > 1:4193660/1‑60 (MQ=255)
tCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGa > 1:1607789/1‑60 (MQ=255)
tCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGa > 1:2747393/1‑60 (MQ=255)
tCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttatt > 1:5294079/1‑70 (MQ=255)
cATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta > 1:4421716/1‑71 (MQ=255)
cATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta > 1:5339176/1‑71 (MQ=255)
ttCGAAAAGGGAATGATGCAATGATAATTGCCACAACCt < 1:995274/39‑1 (MQ=255)
ttCGAAAAGGGAATGATGCAATGATAATTGCCACAACCt < 1:5263173/39‑1 (MQ=255)
ttCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTAt < 1:891257/41‑1 (MQ=255)
ttCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACa > 1:5173014/1‑71 (MQ=255)
ttCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACa > 1:872241/1‑71 (MQ=255)
tCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTAtttt > 1:323492/1‑43 (MQ=255)
tCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTAttt > 1:3231002/1‑42 (MQ=255)
gAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttatt < 1:114137/64‑1 (MQ=255)
gAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttatt < 1:679851/64‑1 (MQ=255)
gAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACatat > 1:1625953/1‑71 (MQ=255)
gAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACatat > 1:1964584/1‑71 (MQ=255)
gAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACata > 1:5003862/1‑70 (MQ=255)
aaaaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt < 1:793100/59‑1 (MQ=255)
aaaGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATgg < 1:3372380/55‑1 (MQ=255)
aaGTGAATGATGCAATGATAATTGCCACAACCTAt < 1:3150284/35‑1 (MQ=38)
aaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttta > 1:995966/1‑59 (MQ=255)
aaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttta > 1:4466968/1‑59 (MQ=255)
aaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtattat < 1:3013766/71‑1 (MQ=255)
aaGGGAATGAAGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtattat < 1:1413985/71‑1 (MQ=255)
ggAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTgg < 1:3669863/71‑1 (MQ=255)
gAATGATGCAATGATAATTGCCACAACCTATTTTTACCa > 1:2306604/1‑39 (MQ=255)
aaTGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt < 1:1615142/70‑1 (MQ=255)
atgatgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGa < 1:4393378/71‑1 (MQ=255)
tgatgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt < 1:2260883/50‑1 (MQ=255)
tgatgCAATGATAATTGCCACAACCTATTTTTAcc < 1:1488915/35‑1 (MQ=255)
tgatgCAATGATAATTGCCACAACCTATTTTTAcc < 1:3085218/35‑1 (MQ=255)
tgatgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGaa < 1:3958978/71‑1 (MQ=255)
gatgCGATGATAATTGCCACAACCTATTTTTACCa > 1:3783535/1‑35 (MQ=255)
gatgCGATGATAATTGCCACAACCTATTTTTACCa > 1:3240065/1‑35 (MQ=255)
atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta > 1:1331182/1‑54 (MQ=255)
atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta > 1:1568456/1‑54 (MQ=255)
atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttta > 1:1840579/1‑50 (MQ=255)
atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttta > 1:2496606/1‑50 (MQ=255)
atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttta > 1:3750306/1‑50 (MQ=255)
atgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt < 1:3116121/66‑1 (MQ=255)
atgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt < 1:4528001/66‑1 (MQ=255)
atgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt < 1:4534430/66‑1 (MQ=255)
atgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATg < 1:911028/71‑1 (MQ=255)
|
CGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATG > minE/2823573‑2823694
|
| 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
