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Pythium aphanidermatum vs Pythium arrhenomanes LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Pythium arrhenomanes (Pythium arrhenomanes ATCC 12531, par_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 arrhenomanes
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 38,716 alignment blocks

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

Uncovered: 12,009,775 out of 35,876,849
Covered: 23,867,074 out of 35,876,849

Uncovered: 1,657,997 out of 18,015,574
Matches: 11,117,861 out of 18,015,574
Mismatches: 4,846,274 out of 18,015,574
Insertions: 393,442 out of 18,015,574
Identity over aligned base-pairs: 68.0%

Pythium arrhenomanes

Uncovered: 19,376,678 out of 44,672,625
Covered: 25,295,947 out of 44,672,625

Uncovered: 2,030,916 out of 18,367,184
Matches: 10,994,790 out of 18,367,184
Mismatches: 4,776,805 out of 18,367,184
Insertions: 564,673 out of 18,367,184
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 38,716 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
173
916.0 bp
10 bp - 100 bp
3,843
252.9 kb
1,263
91.0 kb
100 bp - 1 kb
25,269
10.7 Mb
10,191
4.5 Mb
1 kb - 10 kb
9,411
18.1 Mb
6,360
17.7 Mb
10 kb - 100 kb
20
248.3 kb
453
7.1 Mb