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Pythium aphanidermatum vs Pythium irregulare LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 36,111 alignment blocks

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

Uncovered: 16,775,124 out of 35,876,849
Covered: 19,101,725 out of 35,876,849

Uncovered: 3,374,497 out of 18,015,574
Matches: 9,746,559 out of 18,015,574
Mismatches: 4,484,362 out of 18,015,574
Insertions: 410,156 out of 18,015,574
Identity over aligned base-pairs: 66.6%

Pythium irregulare

Uncovered: 23,060,004 out of 42,968,084
Covered: 19,908,080 out of 42,968,084

Uncovered: 4,786,213 out of 20,543,058
Matches: 10,141,424 out of 20,543,058
Mismatches: 4,879,522 out of 20,543,058
Insertions: 735,899 out of 20,543,058
Identity over aligned base-pairs: 64.4%

Block size distribution

Size range All 36,111 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
137
758.0 bp
10 bp - 100 bp
3,986
264.3 kb
802
56.5 kb
100 bp - 1 kb
24,933
10.4 Mb
7,029
3.2 Mb
1 kb - 10 kb
7,038
12.3 Mb
5,193
14.4 Mb
10 kb - 100 kb
17
218.4 kb
332
5.5 Mb