In this section

Pythium ultimum vs Pythium iwayamai LastZ results

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

Statistics over 45,758 alignment blocks

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

Uncovered: 16,696,690 out of 44,913,582
Covered: 28,216,892 out of 44,913,582

Uncovered: 1,932,487 out of 19,826,256
Matches: 12,693,752 out of 19,826,256
Mismatches: 4,719,753 out of 19,826,256
Insertions: 480,264 out of 19,826,256
Identity over aligned base-pairs: 70.9%

Pythium iwayamai

Uncovered: 17,627,527 out of 43,199,174
Covered: 25,571,647 out of 43,199,174

Uncovered: 1,757,608 out of 19,552,457
Matches: 12,618,312 out of 19,552,457
Mismatches: 4,643,952 out of 19,552,457
Insertions: 532,585 out of 19,552,457
Identity over aligned base-pairs: 70.9%

Block size distribution

Size range All 45,758 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
210
1.2 kb
10 bp - 100 bp
4,517
297.5 kb
1,715
121.4 kb
100 bp - 1 kb
31,081
13.0 Mb
13,402
5.5 Mb
1 kb - 10 kb
9,907
19.4 Mb
6,728
19.1 Mb
10 kb - 100 kb
43
584.3 kb
552
8.5 Mb