In this section

Pythium iwayamai vs Phytophthora lateralis LastZ results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Phytophthora lateralis (Phytophthora lateralis MPF4, MPF4_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium iwayamai 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 iwayamaiPhytophthora lateralis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 44,086 alignment blocks

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

Uncovered: 25,499,357 out of 43,199,174
Covered: 17,699,817 out of 43,199,174

Uncovered: 6,245,950 out of 19,552,457
Matches: 8,690,878 out of 19,552,457
Mismatches: 4,049,115 out of 19,552,457
Insertions: 566,514 out of 19,552,457
Identity over aligned base-pairs: 65.3%

Phytophthora lateralis

Uncovered: 24,634,668 out of 43,981,379
Covered: 19,346,711 out of 43,981,379

Uncovered: 3,570,439 out of 14,242,768
Matches: 7,100,023 out of 14,242,768
Mismatches: 3,254,911 out of 14,242,768
Insertions: 317,395 out of 14,242,768
Identity over aligned base-pairs: 66.5%

Block size distribution

Size range All 44,086 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
181
915.0 bp
10 bp - 100 bp
4,693
318.2 kb
1,456
106.4 kb
100 bp - 1 kb
32,877
13.0 Mb
14,314
5.9 Mb
1 kb - 10 kb
6,320
10.8 Mb
6,640
15.9 Mb
10 kb - 100 kb
15
193.9 kb
166
2.3 Mb