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 |
|
A28 F999 I0 R1
|
113 |
27.6 |
2102982 |
97.5% |
2050407 |
48.6 |
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 | . | 93.9%
| 118.6
/ 4.2
| 33 | coding (928/1017 nt) | waaJ | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/2); new base . (19/12); total (19/14) |
| Fisher's exact test for biased strand distribution p-value = 1.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT > NC_000913/3801024‑3801116
|
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt > 1:859293/1‑49 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:771533/49‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:805637/48‑1 (MQ=255)
aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt < 1:341344/48‑1 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa < 1:280189/48‑3 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa < 1:251199/48‑3 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa < 1:1345414/48‑1 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa < 1:1636323/48‑1 (MQ=255)
gagaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:2102894/1‑48 (MQ=39)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt < 1:1008806/47‑1 (MQ=39)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa < 1:1134187/49‑1 (MQ=39)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa < 1:233855/49‑1 (MQ=39)
atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat < 1:481961/49‑1 (MQ=39)
tataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata < 1:995056/49‑1 (MQ=39)
ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa > 1:555302/1‑49 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt > 1:1731999/1‑48 (MQ=39)
tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa < 1:1904607/49‑1 (MQ=39)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt > 1:1121348/1‑49 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc < 1:1931059/48‑1 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:1131345/1‑49 (MQ=39)
tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:895976/1‑48 (MQ=39)
tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:698809/1‑48 (MQ=39)
cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt < 1:872791/49‑1 (MQ=39)
cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct > 1:184250/1‑49 (MQ=39)
cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct > 1:1615784/1‑49 (MQ=39)
aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg > 1:371747/1‑49 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc < 1:1262443/47‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc < 1:142692/47‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg < 1:2064804/48‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt > 1:85554/1‑49 (MQ=39)
aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:308523/1‑48 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:460880/1‑46 (MQ=39)
tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:260511/1‑49 (MQ=39)
ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:1977159/1‑48 (MQ=39)
tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTc < 1:1596910/48‑1 (MQ=39)
tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa > 1:448747/1‑49 (MQ=39)
tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa > 1:1150597/1‑49 (MQ=39)
tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa > 1:143941/1‑49 (MQ=39)
atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt > 1:1788023/1‑49 (MQ=39)
|
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT > NC_000913/3801024‑3801116
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
