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Pythium iwayamai vs Pythium vexans LastZ results

Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) and Pythium vexans (Pythium vexans DAOM BR484, pve_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Pythium iwayamai 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 iwayamaiPythium vexans
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 39,491 alignment blocks

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

Uncovered: 22,280,346 out of 43,199,174
Covered: 20,918,828 out of 43,199,174

Uncovered: 3,834,732 out of 19,552,457
Matches: 10,532,168 out of 19,552,457
Mismatches: 4,506,617 out of 19,552,457
Insertions: 678,940 out of 19,552,457
Identity over aligned base-pairs: 67.0%

Pythium vexans

Uncovered: 13,725,020 out of 33,844,883
Covered: 20,119,863 out of 33,844,883

Uncovered: 3,329,785 out of 18,608,353
Matches: 10,270,277 out of 18,608,353
Mismatches: 4,495,748 out of 18,608,353
Insertions: 512,543 out of 18,608,353
Identity over aligned base-pairs: 67.2%

Block size distribution

Size range All 39,491 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
105
480.0 bp
10 bp - 100 bp
4,005
266.8 kb
1,256
87.4 kb
100 bp - 1 kb
28,088
11.6 Mb
10,852
4.5 Mb
1 kb - 10 kb
7,273
13.0 Mb
6,225
17.1 Mb
10 kb - 100 kb
20
254.5 kb
236
3.4 Mb