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Phytophthora parasitica vs Giardia intestinalis - GCA_000002435.2 LastZ results

Phytophthora parasitica (Phytophthora parasitica P1569, Phyt_para_P1569_V1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Phytophthora parasitica 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

ParameterPhytophthora parasiticaGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,572 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Phytophthora parasitica

Uncovered: 54,622,750 out of 55,229,644
Covered: 606,894 out of 55,229,644

Uncovered: 27,011,266 out of 27,601,672
Matches: 347,954 out of 27,601,672
Mismatches: 220,232 out of 27,601,672
Insertions: 22,220 out of 27,601,672
Identity over aligned base-pairs: 58.9%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,678,937 out of 12,078,186
Covered: 399,249 out of 12,078,186

Uncovered: 9,075,684 out of 9,469,365
Matches: 229,605 out of 9,469,365
Mismatches: 143,978 out of 9,469,365
Insertions: 20,098 out of 9,469,365
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 1,572 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
4
23.0 bp
10 bp - 100 bp
182
13.3 kb
79
6.1 kb
100 bp - 1 kb
1,243
478.9 kb
717
331.1 kb
1 kb - 10 kb
143
212.9 kb
197
368.0 kb