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Pythium aphanidermatum vs Phytophthora parasitica LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium aphanidermatum 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 aphanidermatumPhytophthora parasitica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,993 alignment blocks

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

Uncovered: 18,116,493 out of 35,876,849
Covered: 17,760,356 out of 35,876,849

Uncovered: 4,310,200 out of 18,015,574
Matches: 8,821,176 out of 18,015,574
Mismatches: 4,386,972 out of 18,015,574
Insertions: 497,226 out of 18,015,574
Identity over aligned base-pairs: 64.4%

Phytophthora parasitica

Uncovered: 33,448,569 out of 55,229,644
Covered: 21,781,075 out of 55,229,644

Uncovered: 10,220,004 out of 27,601,672
Matches: 10,860,106 out of 27,601,672
Mismatches: 5,881,080 out of 27,601,672
Insertions: 640,482 out of 27,601,672
Identity over aligned base-pairs: 62.5%

Block size distribution

Size range All 38,993 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
133
671.0 bp
10 bp - 100 bp
3,791
256.1 kb
908
65.7 kb
100 bp - 1 kb
27,274
11.5 Mb
9,528
4.4 Mb
1 kb - 10 kb
7,779
13.2 Mb
6,637
16.7 Mb
10 kb - 100 kb
16
194.3 kb
266
4.1 Mb