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 |
|
A22 F999 I0 R1
|
108 |
38.1 |
2810592 |
98.4% |
2765622 |
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 | . | 97.8%
| 201.2
/ ‑1.2
| 46 | coding (928/1017 nt) | waaJ | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base . (17/28); total (17/29) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCA > NC_000913/3801024‑3801115
|
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt < 1:2095453/50‑1 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtt > 1:472452/1‑50 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:1096812/49‑1 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:1944814/49‑1 (MQ=255)
tataATTCCTGTGATATAATGATGTTGCACTAAAAGATGTTTATATCttt > 1:1675227/1‑50 (MQ=255)
ataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt > 1:320229/1‑50 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt > 1:1304936/1‑50 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt > 1:2124358/1‑50 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttt < 1:1873677/49‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:1337859/48‑1 (MQ=255)
taATTCCGGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt < 1:730272/50‑1 (MQ=255)
aaTTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttttt > 1:323169/1‑49 (MQ=255)
actCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttt < 1:1857008/47‑1 (MQ=255)
ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta > 1:1262085/1‑48 (MQ=255)
ccTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa < 1:1701908/49‑1 (MQ=255)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTc < 1:2284673/48‑1 (MQ=39)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa < 1:1076450/50‑1 (MQ=255)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCa < 1:1810615/49‑1 (MQ=39)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat < 1:897991/50‑1 (MQ=255)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat < 1:606542/50‑1 (MQ=255)
gaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaat < 1:77051/50‑1 (MQ=255)
atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata < 1:2193248/50‑1 (MQ=255)
atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaata < 1:1441678/50‑1 (MQ=255)
ataATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat > 1:743265/1‑50 (MQ=255)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat < 1:217645/49‑1 (MQ=39)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaataat < 1:1551866/49‑1 (MQ=39)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt < 1:1251349/50‑1 (MQ=255)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt > 1:695072/1‑50 (MQ=255)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt < 1:2718450/50‑1 (MQ=255)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt < 1:2425996/50‑1 (MQ=255)
taATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAAtt < 1:1131356/50‑1 (MQ=255)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTg < 1:2693113/49‑1 (MQ=39)
atgatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGa > 1:1820045/1‑50 (MQ=255)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt < 1:2776041/50‑1 (MQ=255)
tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc < 1:1661495/50‑1 (MQ=255)
gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt > 1:863500/1‑50 (MQ=255)
cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc > 1:1632753/1‑50 (MQ=255)
cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt < 1:989151/49‑1 (MQ=39)
cACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAt < 1:1275281/49‑1 (MQ=39)
aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtct < 1:1447335/50‑1 (MQ=255)
cTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc < 1:1519303/50‑1 (MQ=255)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg > 1:2670424/1‑50 (MQ=255)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg > 1:1903453/1‑50 (MQ=255)
aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt > 1:1738565/1‑50 (MQ=255)
aaaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt > 1:385774/1‑50 (MQ=255)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg < 1:159625/48‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:2580637/1‑50 (MQ=255)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg < 1:1863126/50‑1 (MQ=255)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg < 1:1777974/50‑1 (MQ=255)
aaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:1233337/1‑49 (MQ=39)
aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:2078291/1‑48 (MQ=39)
aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga < 1:367490/50‑1 (MQ=255)
aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga < 1:1272563/50‑1 (MQ=255)
gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:1707492/1‑47 (MQ=39)
gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:1737495/1‑47 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga > 1:2692126/1‑48 (MQ=39)
aTGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga > 1:239607/1‑48 (MQ=39)
gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:1652929/1‑50 (MQ=255)
tttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt < 1:677799/49‑1 (MQ=39)
tataTC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCa < 1:1521179/49‑1 (MQ=39)
|
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCA > NC_000913/3801024‑3801115
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
