In this section

Pythium irregulare vs Pythium vexans LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium irregulare 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 irregularePythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 35,606 alignment blocks

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

Uncovered: 21,397,898 out of 42,968,084
Covered: 21,570,186 out of 42,968,084

Uncovered: 3,839,643 out of 20,543,058
Matches: 11,097,046 out of 20,543,058
Mismatches: 4,836,518 out of 20,543,058
Insertions: 769,851 out of 20,543,058
Identity over aligned base-pairs: 66.4%

Pythium vexans

Uncovered: 13,268,949 out of 33,844,883
Covered: 20,575,934 out of 33,844,883

Uncovered: 2,809,241 out of 18,608,353
Matches: 10,704,768 out of 18,608,353
Mismatches: 4,601,879 out of 18,608,353
Insertions: 492,465 out of 18,608,353
Identity over aligned base-pairs: 67.8%

Block size distribution

Size range All 35,606 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
123
679.0 bp
10 bp - 100 bp
3,715
245.9 kb
1,120
78.5 kb
100 bp - 1 kb
23,704
10.1 Mb
8,052
3.6 Mb
1 kb - 10 kb
8,041
14.6 Mb
5,400
15.4 Mb
10 kb - 100 kb
23
310.7 kb
388
6.2 Mb