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Pythium aphanidermatum vs Giardia intestinalis - GCA_000002435.2 LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Giardia intestinalis - GCA_000002435.2 (Giardia intestinalis, GCA000002435v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 114. Pythium aphanidermatum 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 aphanidermatumGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,578 alignment blocks

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

Uncovered: 35,253,517 out of 35,876,849
Covered: 623,332 out of 35,876,849

Uncovered: 17,459,774 out of 18,015,574
Matches: 326,245 out of 18,015,574
Mismatches: 206,914 out of 18,015,574
Insertions: 22,641 out of 18,015,574
Identity over aligned base-pairs: 58.7%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,661,159 out of 12,078,186
Covered: 417,027 out of 12,078,186

Uncovered: 9,059,286 out of 9,469,365
Matches: 234,725 out of 9,469,365
Mismatches: 154,488 out of 9,469,365
Insertions: 20,866 out of 9,469,365
Identity over aligned base-pairs: 57.2%

Block size distribution

Size range All 1,578 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1
4.0 bp
10 bp - 100 bp
187
13.0 kb
70
5.0 kb
100 bp - 1 kb
1,228
476.7 kb
733
329.1 kb
1 kb - 10 kb
162
243.6 kb
208
399.3 kb