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 |
|
A8 F999 I0 R1
|
76 |
68.2 |
5140122 |
96.8% |
4975638 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,801,078 |
(T)7→6 |
coding (922/1017 nt) |
waaJ ← |
UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,801,072 | 0 | T | . | 95.9%
| 209.2
/ 4.7
| 49 | coding (928/1017 nt) | waaJ | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base . (22/25); total (23/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01 |
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT > NC_000913/3801024‑3801116
|
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt > 1:5103663/1‑50 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt < 1:4517088/50‑1 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt < 1:4159761/50‑1 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:1069990/49‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt < 1:3962568/50‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:1403657/48‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGAAGTTTATATCttttt < 1:1090763/50‑1 (MQ=255)
aaTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt > 1:2090225/1‑49 (MQ=255)
aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta < 1:3029461/50‑2 (MQ=255)
aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta < 1:4656212/50‑2 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat > 1:1986492/1‑49 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat < 1:1907923/49‑2 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:3838415/1‑50 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:1053515/1‑50 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:1976461/1‑50 (MQ=255)
tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:4873028/1‑49 (MQ=39)
gagaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc > 1:3833725/1‑49 (MQ=39)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc < 1:62675/48‑1 (MQ=39)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa < 1:3189186/50‑1 (MQ=255)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa < 1:3454362/49‑1 (MQ=39)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat < 1:3783948/50‑1 (MQ=255)
atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata < 1:2864643/50‑1 (MQ=255)
tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa < 1:1235371/50‑1 (MQ=255)
ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat > 1:1999666/1‑50 (MQ=255)
ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat > 1:3602358/1‑50 (MQ=255)
ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat > 1:3859130/1‑50 (MQ=255)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat < 1:1018165/49‑1 (MQ=39)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat < 1:3907360/49‑1 (MQ=39)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt < 1:1404578/50‑1 (MQ=255)
aaTGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt > 1:1616406/1‑49 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa < 1:1521986/50‑1 (MQ=255)
tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt < 1:2508795/50‑1 (MQ=255)
gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt > 1:1911007/1‑50 (MQ=255)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt > 1:690897/1‑50 (MQ=255)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt < 1:4791535/50‑1 (MQ=255)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt > 1:2107030/1‑50 (MQ=255)
tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc < 1:3933298/50‑1 (MQ=255)
tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc < 1:792277/50‑1 (MQ=255)
gTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:4274258/1‑50 (MQ=255)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg < 1:1374282/49‑1 (MQ=39)
gCACTAAGAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa < 1:1383681/49‑1 (MQ=38)
gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa < 1:432786/49‑1 (MQ=39)
gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCa < 1:2034214/49‑1 (MQ=39)
gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt > 1:2096372/1‑50 (MQ=255)
aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct > 1:1162886/1‑50 (MQ=255)
cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc > 1:3336989/1‑50 (MQ=255)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg > 1:2972330/1‑50 (MQ=255)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt < 1:397223/49‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt < 1:4670658/49‑1 (MQ=39)
aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg < 1:4485774/50‑1 (MQ=255)
aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg < 1:3089496/50‑1 (MQ=255)
aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg < 1:117320/50‑1 (MQ=255)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga < 1:1131692/50‑1 (MQ=255)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga > 1:4912690/1‑48 (MQ=39)
tttttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag > 1:3238856/3‑50 (MQ=255)
tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag > 1:4638892/1‑50 (MQ=255)
gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:3931057/1‑50 (MQ=255)
tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:4016165/1‑49 (MQ=39)
atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt < 1:1871852/49‑1 (MQ=39)
|
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT > NC_000913/3801024‑3801116
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
