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Hyaloperonospora arabidopsidis vs Emiliania huxleyi LastZ results

Hyaloperonospora arabidopsidis (Hyaloperonospora arabidopsidis, HyaAraEmoy2_2.0) and Emiliania huxleyi (Emiliania huxleyi CCMP1516, Emiliana_huxleyi_CCMP1516_main_genome_assembly_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 109. Hyaloperonospora arabidopsidis 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

ParameterHyaloperonospora arabidopsidisEmiliania huxleyi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 11,977 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Hyaloperonospora arabidopsidis

Uncovered: 77,319,203 out of 78,897,814
Covered: 1,578,611 out of 78,897,814

Uncovered: 11,831,717 out of 13,171,834
Matches: 816,772 out of 13,171,834
Mismatches: 477,048 out of 13,171,834
Insertions: 46,297 out of 13,171,834
Identity over aligned base-pairs: 60.9%

Emiliania huxleyi

Uncovered: 164,975,059 out of 167,675,649
Covered: 2,700,590 out of 167,675,649

Uncovered: 37,534,316 out of 39,740,234
Matches: 1,369,725 out of 39,740,234
Mismatches: 747,968 out of 39,740,234
Insertions: 88,225 out of 39,740,234
Identity over aligned base-pairs: 62.1%

Block size distribution

Size range All 11,977 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
36
189.0 bp
10 bp - 100 bp
2,895
203.1 kb
512
37.2 kb
100 bp - 1 kb
8,681
2.5 Mb
4,053
1.6 Mb
1 kb - 10 kb
364
510.8 kb
931
1.6 Mb
10 kb - 100 kb
1
12.6 kb
1
20.7 kb