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 |
|
A26 F999 I0 R1
|
111 |
30.9 |
2867207 |
97.9% |
2806995 |
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 | . | 97.7%
| 177.9
/ ‑0.8
| 44 | coding (928/1017 nt) | waaJ | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base . (28/15); total (29/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT > NC_000913/3801024‑3801116
|
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:1332490/49‑1 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt > 1:1405317/1‑49 (MQ=255)
tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt > 1:365984/1‑49 (MQ=255)
tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt > 1:259367/1‑49 (MQ=255)
tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt > 1:1294557/1‑49 (MQ=255)
tataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt > 1:2676418/1‑49 (MQ=255)
ataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt > 1:1139312/1‑49 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt < 1:1204137/47‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt < 1:1266830/47‑1 (MQ=255)
aTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt < 1:2146921/48‑1 (MQ=255)
ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta < 1:1238087/49‑2 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa < 1:731365/48‑3 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttttaa < 1:676686/48‑3 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa > 1:2138968/1‑49 (MQ=255)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa < 1:2702571/49‑1 (MQ=39)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa < 1:1098535/49‑1 (MQ=39)
atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa > 1:2785821/1‑48 (MQ=39)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataa < 1:2087849/48‑1 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt > 1:1059823/1‑48 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt > 1:2507367/1‑48 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg < 1:708598/49‑1 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg < 1:1112726/49‑1 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg < 1:455959/49‑1 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg < 1:339046/49‑1 (MQ=39)
tgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa < 1:2532869/49‑1 (MQ=39)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAtt > 1:2583729/1‑49 (MQ=39)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt < 1:2241969/48‑1 (MQ=39)
tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt < 1:240626/49‑1 (MQ=39)
gTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc > 1:941048/1‑49 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc < 1:2191053/48‑1 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:1766152/1‑49 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg < 1:1448693/49‑1 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:1467185/1‑49 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg < 1:1964833/49‑1 (MQ=39)
aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc < 1:2653225/49‑1 (MQ=39)
cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct < 1:1743376/49‑1 (MQ=39)
cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct > 1:1284664/1‑49 (MQ=39)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc > 1:2632900/1‑49 (MQ=39)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc > 1:1804544/1‑49 (MQ=39)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc > 1:2839569/1‑49 (MQ=39)
aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg > 1:1709302/1‑49 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt > 1:169969/1‑49 (MQ=39)
aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:2805610/1‑49 (MQ=39)
aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:1048211/1‑48 (MQ=39)
gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:1196758/1‑47 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:549071/1‑46 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:1907235/1‑46 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:211147/1‑46 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:7787/1‑46 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:922848/1‑46 (MQ=39)
tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga > 1:378104/1‑47 (MQ=39)
tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:1689919/1‑49 (MQ=39)
ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:1273131/1‑48 (MQ=39)
ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:812829/1‑48 (MQ=39)
tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa > 1:59573/1‑49 (MQ=39)
atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt > 1:1495022/1‑49 (MQ=39)
atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt > 1:221569/1‑49 (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
