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Pythium ultimum vs Pythium irregulare LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium ultimum 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 ultimumPythium irregulare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 40,002 alignment blocks

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

Uncovered: 15,386,088 out of 44,913,582
Covered: 29,527,494 out of 44,913,582

Uncovered: 1,078,175 out of 19,826,256
Matches: 13,668,687 out of 19,826,256
Mismatches: 4,675,742 out of 19,826,256
Insertions: 403,652 out of 19,826,256
Identity over aligned base-pairs: 72.9%

Pythium irregulare

Uncovered: 15,339,747 out of 42,968,084
Covered: 27,628,337 out of 42,968,084

Uncovered: 1,369,044 out of 20,543,058
Matches: 13,649,898 out of 20,543,058
Mismatches: 4,830,816 out of 20,543,058
Insertions: 693,300 out of 20,543,058
Identity over aligned base-pairs: 71.2%

Block size distribution

Size range All 40,002 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
199
1.0 kb
10 bp - 100 bp
4,691
303.7 kb
2,003
137.7 kb
100 bp - 1 kb
24,172
10.2 Mb
9,676
4.2 Mb
1 kb - 10 kb
10,870
23.0 Mb
5,345
14.9 Mb
10 kb - 100 kb
70
954.2 kb
752
15.2 Mb