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Pythium irregulare vs Giardia intestinalis - GCA_000002435.2 LastZ results

Pythium irregulare (Globisporangium irregulare DAOM BR486, pir_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 irregulare 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 irregulareGiardia intestinalis - GCA_000002435.2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,668 alignment blocks

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

Uncovered: 42,363,798 out of 42,968,084
Covered: 604,286 out of 42,968,084

Uncovered: 19,999,386 out of 20,543,058
Matches: 321,410 out of 20,543,058
Mismatches: 201,022 out of 20,543,058
Insertions: 21,240 out of 20,543,058
Identity over aligned base-pairs: 59.1%

Giardia intestinalis - GCA_000002435.2

Uncovered: 11,679,473 out of 12,078,186
Covered: 398,713 out of 12,078,186

Uncovered: 9,076,522 out of 9,469,365
Matches: 229,076 out of 9,469,365
Mismatches: 144,137 out of 9,469,365
Insertions: 19,630 out of 9,469,365
Identity over aligned base-pairs: 58.3%

Block size distribution

Size range All 1,668 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3
17.0 bp
10 bp - 100 bp
231
15.9 kb
86
6.1 kb
100 bp - 1 kb
1,288
474.6 kb
741
323.9 kb
1 kb - 10 kb
146
225.8 kb
196
386.5 kb