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Phytophthora ramorum vs Pythium vexans LastZ results

Phytophthora ramorum (Phytophthora ramorum, ASM14973v1) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Phytophthora ramorum 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

ParameterPhytophthora ramorumPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 40,083 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora ramorum

Uncovered: 40,050,515 out of 66,652,401
Covered: 26,601,886 out of 66,652,401

Uncovered: 4,879,712 out of 22,377,278
Matches: 11,824,461 out of 22,377,278
Mismatches: 5,100,784 out of 22,377,278
Insertions: 572,321 out of 22,377,278
Identity over aligned base-pairs: 67.6%

Pythium vexans

Uncovered: 12,084,211 out of 33,844,883
Covered: 21,760,672 out of 33,844,883

Uncovered: 2,472,657 out of 18,608,353
Matches: 10,363,521 out of 18,608,353
Mismatches: 5,174,795 out of 18,608,353
Insertions: 597,380 out of 18,608,353
Identity over aligned base-pairs: 64.2%

Block size distribution

Size range All 40,083 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
151
754.0 bp
10 bp - 100 bp
4,022
265.8 kb
1,251
87.6 kb
100 bp - 1 kb
25,862
11.1 Mb
9,140
4.1 Mb
1 kb - 10 kb
10,000
18.8 Mb
6,489
17.6 Mb
10 kb - 100 kb
48
721.1 kb
535
9.1 Mb