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Pythium aphanidermatum vs Guillardia theta CCMP2712 LastZ results

Pythium aphanidermatum (Pythium aphanidermatum DAOM BR444, pag1_scaffolds_v1) and Guillardia theta CCMP2712 (Guillardia theta CCMP2712, Guith1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Protists release 111. 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 aphanidermatumGuillardia theta CCMP2712
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 8,183 alignment blocks

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

Uncovered: 33,675,974 out of 35,876,849
Covered: 2,200,875 out of 35,876,849

Uncovered: 16,085,106 out of 18,015,574
Matches: 1,172,739 out of 18,015,574
Mismatches: 675,185 out of 18,015,574
Insertions: 82,544 out of 18,015,574
Identity over aligned base-pairs: 60.7%

Guillardia theta CCMP2712

Uncovered: 84,959,611 out of 87,266,873
Covered: 2,307,262 out of 87,266,873

Uncovered: 28,597,929 out of 30,644,092
Matches: 1,232,643 out of 30,644,092
Mismatches: 722,417 out of 30,644,092
Insertions: 91,103 out of 30,644,092
Identity over aligned base-pairs: 60.2%

Block size distribution

Size range All 8,183 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
37
192.0 bp
10 bp - 100 bp
1,836
127.1 kb
446
32.1 kb
100 bp - 1 kb
5,702
2.0 Mb
2,804
1.2 Mb
1 kb - 10 kb
607
989.5 kb
938
1.7 Mb
10 kb - 100 kb
1
10.0 kb
15
180.4 kb