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Pythium aphanidermatum vs Pythium vexans LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 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 aphanidermatumPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 31,542 alignment blocks

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

Uncovered: 17,561,826 out of 35,876,849
Covered: 18,315,023 out of 35,876,849

Uncovered: 3,960,815 out of 18,015,574
Matches: 9,167,193 out of 18,015,574
Mismatches: 4,397,411 out of 18,015,574
Insertions: 490,155 out of 18,015,574
Identity over aligned base-pairs: 65.2%

Pythium vexans

Uncovered: 15,215,213 out of 33,844,883
Covered: 18,629,670 out of 33,844,883

Uncovered: 4,145,392 out of 18,608,353
Matches: 9,254,346 out of 18,608,353
Mismatches: 4,602,634 out of 18,608,353
Insertions: 605,981 out of 18,608,353
Identity over aligned base-pairs: 64.0%

Block size distribution

Size range All 31,542 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
86
422.0 bp
10 bp - 100 bp
3,083
208.5 kb
787
55.2 kb
100 bp - 1 kb
21,361
9.2 Mb
6,363
2.9 Mb
1 kb - 10 kb
6,996
12.3 Mb
4,895
13.4 Mb
10 kb - 100 kb
16
206.0 kb
343
5.6 Mb