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Hyaloperonospora arabidopsidis vs Pythium irregulare LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 33,975 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 62,814,098 out of 78,897,814
Covered: 16,083,716 out of 78,897,814

Uncovered: 3,895,502 out of 13,171,834
Matches: 6,096,650 out of 13,171,834
Mismatches: 2,901,500 out of 13,171,834
Insertions: 278,182 out of 13,171,834
Identity over aligned base-pairs: 65.7%

Pythium irregulare

Uncovered: 29,801,569 out of 42,968,084
Covered: 13,166,515 out of 42,968,084

Uncovered: 9,990,072 out of 20,543,058
Matches: 6,695,464 out of 20,543,058
Mismatches: 3,468,856 out of 20,543,058
Insertions: 388,666 out of 20,543,058
Identity over aligned base-pairs: 63.4%

Block size distribution

Size range All 33,975 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
128
682.0 bp
10 bp - 100 bp
4,350
288.1 kb
1,294
86.2 kb
100 bp - 1 kb
24,248
9.7 Mb
9,363
4.3 Mb
1 kb - 10 kb
5,236
9.1 Mb
5,404
13.0 Mb
10 kb - 100 kb
13
216.0 kb
130
2.0 Mb