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Pythium ultimum vs Pythium aphanidermatum LastZ results

Pythium ultimum (Globisporangium iwayamae DAOM BR242034, pug) and Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_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 aphanidermatum
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 36,478 alignment blocks

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

Uncovered: 22,980,400 out of 44,913,582
Covered: 21,933,182 out of 44,913,582

Uncovered: 3,995,821 out of 19,826,256
Matches: 10,177,699 out of 19,826,256
Mismatches: 5,004,968 out of 19,826,256
Insertions: 647,768 out of 19,826,256
Identity over aligned base-pairs: 64.3%

Pythium aphanidermatum

Uncovered: 16,413,931 out of 35,876,849
Covered: 19,462,918 out of 35,876,849

Uncovered: 3,356,449 out of 18,015,574
Matches: 9,618,884 out of 18,015,574
Mismatches: 4,597,787 out of 18,015,574
Insertions: 442,454 out of 18,015,574
Identity over aligned base-pairs: 65.6%

Block size distribution

Size range All 36,478 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
146
722.0 bp
10 bp - 100 bp
3,807
254.4 kb
920
64.8 kb
100 bp - 1 kb
24,719
10.4 Mb
6,789
3.0 Mb
1 kb - 10 kb
7,781
14.1 Mb
4,688
12.8 Mb
10 kb - 100 kb
25
339.2 kb
468
9.2 Mb
100 kb - 1 Mb
1
106.8 kb