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Phaeodactylum tricornutum vs Pythium iwayamai LastZ results

Phaeodactylum tricornutum (Phaeodactylum tricornutum CCAP 1055/1, ASM15095v2) and Pythium iwayamai (Pythium iwayamai DAOM BR242034, piw_scaffolds_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. Phaeodactylum tricornutum 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

ParameterPhaeodactylum tricornutumPythium iwayamai
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 5,562 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phaeodactylum tricornutum

Uncovered: 25,851,797 out of 27,568,093
Covered: 1,716,296 out of 27,568,093

Uncovered: 16,224,374 out of 17,873,974
Matches: 986,180 out of 17,873,974
Mismatches: 596,754 out of 17,873,974
Insertions: 66,666 out of 17,873,974
Identity over aligned base-pairs: 59.8%

Pythium iwayamai

Uncovered: 41,404,792 out of 43,199,174
Covered: 1,794,382 out of 43,199,174

Uncovered: 17,966,575 out of 19,552,457
Matches: 962,559 out of 19,552,457
Mismatches: 567,152 out of 19,552,457
Insertions: 56,171 out of 19,552,457
Identity over aligned base-pairs: 60.7%

Block size distribution

Size range All 5,562 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
10
39.0 bp
10 bp - 100 bp
859
61.4 kb
195
14.6 kb
100 bp - 1 kb
4,273
1.5 Mb
2,166
986.9 kb
1 kb - 10 kb
420
608.7 kb
723
1.2 Mb