In this section

Pythium ultimum vs Pythium vexans LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium ultimum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterPythium ultimumPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 35,687 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Pythium ultimum

Uncovered: 22,169,934 out of 44,913,582
Covered: 22,743,648 out of 44,913,582

Uncovered: 3,331,752 out of 19,826,256
Matches: 10,919,516 out of 19,826,256
Mismatches: 4,922,107 out of 19,826,256
Insertions: 652,881 out of 19,826,256
Identity over aligned base-pairs: 66.2%

Pythium vexans

Uncovered: 13,130,332 out of 33,844,883
Covered: 20,714,551 out of 33,844,883

Uncovered: 2,863,872 out of 18,608,353
Matches: 10,473,442 out of 18,608,353
Mismatches: 4,745,859 out of 18,608,353
Insertions: 525,180 out of 18,608,353
Identity over aligned base-pairs: 66.5%

Block size distribution

Size range All 35,687 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
139
740.0 bp
10 bp - 100 bp
3,617
236.4 kb
1,127
78.9 kb
100 bp - 1 kb
23,501
10.0 Mb
8,145
3.3 Mb
1 kb - 10 kb
8,401
15.7 Mb
4,642
12.9 Mb
10 kb - 100 kb
29
406.6 kb
533
10.0 Mb