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 |
|
A27 F999 I0 R1
|
113 |
28.0 |
2125537 |
97.5% |
2072398 |
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 | . | 90.0%
| 95.1
/ 9.0
| 30 | coding (928/1017 nt) | waaJ | UDP‑glucose:(glucosyl)LPS alpha‑1,2‑glucosyltransferase |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base . (16/11); total (17/13) |
| Fisher's exact test for biased strand distribution p-value = 5.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01 |
CTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAT > NC_000913/3801024‑3801116
|
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:895458/49‑1 (MQ=255)
cTATAATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCt < 1:2019193/49‑1 (MQ=255)
ataATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt > 1:1951454/1‑49 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:691517/48‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:525777/48‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:1423695/48‑1 (MQ=255)
taATTCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCttt < 1:172398/48‑1 (MQ=255)
ttCCTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCtttttta < 1:313758/49‑2 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaat > 1:519049/1‑48 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa < 1:989990/48‑1 (MQ=255)
cTGAGATATAATGATGTTGCACTAAAAGATGTTTATATCTTTTTTaaa < 1:1358189/48‑1 (MQ=255)
tGAGATATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:1839979/1‑49 (MQ=39)
gagaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt > 1:1064350/1‑48 (MQ=39)
agaTATAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAAtt < 1:1915512/47‑1 (MQ=39)
atatAATGATGTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCaa > 1:1547377/1‑48 (MQ=39)
gatgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt > 1:1298898/1‑49 (MQ=39)
atgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAt < 1:79003/48‑1 (MQ=39)
tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt > 1:928752/1‑49 (MQ=39)
tgTTGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGAttt > 1:1808205/1‑49 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTc < 1:51678/48‑1 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:1022996/1‑49 (MQ=39)
ttGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg < 1:606264/49‑1 (MQ=39)
tGCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCg > 1:1706999/1‑48 (MQ=39)
gCACTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGc < 1:1383328/48‑1 (MQ=39)
aCTAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtc > 1:1902639/1‑49 (MQ=39)
tAAAAGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc > 1:1053930/1‑49 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCAtctc < 1:1653450/47‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCg < 1:435398/48‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt < 1:118079/49‑1 (MQ=39)
aaaGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGt > 1:1910159/1‑49 (MQ=39)
aGATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTgg < 1:906826/49‑1 (MQ=39)
gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTg > 1:726488/1‑47 (MQ=39)
gATGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGga < 1:984719/49‑1 (MQ=39)
tGTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGgaga < 1:477322/49‑1 (MQ=39)
gTTTATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGagag > 1:25578/1‑49 (MQ=39)
ttATATC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGt > 1:922730/1‑48 (MQ=39)
atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt > 1:541854/1‑49 (MQ=39)
atatC‑TTTTTTAAATTCAATAATTGATTTCGCATCTCGTGGAGAGTCAt > 1:1895744/1‑49 (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
