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 |
|
A2 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,523,433 |
G→T |
37.5% |
A78S (GCC→TCC) |
flk → |
predicted flagella assembly protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,523,433 | 0 | G | T | 37.5%
| 85.9
/ 44.8
| 56 | A78S (GCC→TCC) | flk | predicted flagella assembly protein |
| Reads supporting (aligned to +/- strand): ref base G (11/24); new base T (13/8); total (24/32) |
| Fisher's exact test for biased strand distribution p-value = 4.96e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01 |
AGGCACGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGCTTTT > minE/1523379‑1523500
|
aGGCACGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATa < 1:2663950/67‑1 (MQ=255)
gCACGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTgg < 1:2049751/71‑1 (MQ=255)
gCACGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTgg < 1:146877/71‑1 (MQ=255)
cGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc < 1:1248275/71‑1 (MQ=255)
cGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc < 1:2385471/71‑1 (MQ=255)
cGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc < 1:237852/71‑1 (MQ=255)
cGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc < 1:2876469/71‑1 (MQ=255)
gATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc > 1:3038851/1‑70 (MQ=255)
gATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc > 1:2370732/1‑70 (MQ=255)
gATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcg > 1:3744079/1‑69 (MQ=255)
atatTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCaa > 1:3658241/1‑71 (MQ=255)
atatTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCaa > 1:3405459/1‑71 (MQ=255)
atatTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCaa > 1:3887787/1‑71 (MQ=255)
ggTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCActtcccttcc > 1:3934558/1‑45 (MQ=255)
gTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTctg < 1:3488493/71‑1 (MQ=255)
gggAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGcc > 1:170173/1‑70 (MQ=255)
gggAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCcg > 1:1407626/1‑71 (MQ=255)
gggAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCcg > 1:2495548/1‑71 (MQ=255)
ggAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATat < 1:45771/47‑2 (MQ=255)
ggAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATaa < 1:145828/47‑1 (MQ=255)
gaTTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCgcgc > 1:1327276/1‑70 (MQ=255)
aTTCACCGCTGCTTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGgcgc < 1:2750894/51‑1 (MQ=255)
tCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCaa < 1:3208947/69‑1 (MQ=255)
tCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCaa < 1:3910153/69‑1 (MQ=255)
cGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:2685977/71‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGc > 1:2537060/1‑57 (MQ=255)
gctgctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc > 1:4123441/1‑70 (MQ=255)
gctgctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc > 1:854088/1‑70 (MQ=255)
gctgctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc > 1:2200756/1‑70 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCaaa > 1:2016134/1‑65 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc > 1:1733709/1‑70 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:2303773/70‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:820185/70‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:2796376/70‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc > 1:4195214/1‑70 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:401093/70‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc > 1:1635754/1‑70 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:1703128/70‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:2010616/70‑1 (MQ=255)
gctgctTTCGCGTCACTTCCCTGCCCCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGc < 1:1036284/70‑1 (MQ=255)
tgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGcc > 1:3351968/1‑69 (MQ=255)
tgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCa > 1:336792/1‑70 (MQ=255)
tgctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCa > 1:1971972/1‑70 (MQ=255)
gctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCAtt > 1:1962845/1‑71 (MQ=255)
gctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCAtt > 1:3672338/1‑71 (MQ=255)
ctTTCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCaa > 1:3937933/1‑42 (MQ=255)
ctTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCAt < 1:2963735/69‑1 (MQ=255)
tttCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCaa < 1:3952684/59‑1 (MQ=255)
ttCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCa < 1:1202682/39‑1 (MQ=255)
tCGCGTCACTTCCCTTCCGCTGAGCATAATCTGGCGCa < 1:2405694/38‑1 (MQ=255)
cttcccttccGCTGAGCATAATCTGGCGCAACGTctgc > 1:2933767/1‑38 (MQ=255)
cttcccttccGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTc > 1:3549043/1‑60 (MQ=255)
cttcccttccGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGc > 1:3165408/1‑71 (MQ=255)
cttcccttccGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGc > 1:2109673/1‑71 (MQ=255)
cTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGc < 1:1949304/71‑1 (MQ=255)
ttCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCt < 1:3992767/60‑1 (MQ=255)
ttCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCt < 1:1219196/60‑1 (MQ=255)
ttCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCt < 1:2758799/60‑1 (MQ=255)
ttCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCt < 1:232805/60‑1 (MQ=255)
ccTTCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGCtttt < 1:4158430/71‑1 (MQ=255)
ccTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGCtttt < 1:451379/71‑1 (MQ=255)
|
AGGCACGATATTGGTCTGTCGGGAGATTCACCGCTGCTTTCGCGTCACTTCCCTGCCGCTGAGCATAATCTGGCGCAACGTCTGCTGGCCGCGCAAAAAAGCCATTCTGCCCGCCAGCTTTT > minE/1523379‑1523500
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
