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Oryza sativa Japonica Group vs Cannabis sativa female LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Cannabis sativa female (Cannabis sativa, cs10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. Oryza sativa Japonica Group 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
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
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

ParameterOryza sativa Japonica GroupCannabis sativa female
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 130,118 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 340,143,187 out of 375,049,285
Covered: 34,906,098 out of 375,049,285

Uncovered: 15,120,978 out of 34,818,902
Matches: 12,665,917 out of 34,818,902
Mismatches: 6,600,014 out of 34,818,902
Insertions: 431,993 out of 34,818,902
Identity over aligned base-pairs: 64.3%

Cannabis sativa female

Uncovered: 845,278,190 out of 875,732,045
Covered: 30,453,855 out of 875,732,045

Uncovered: 16,804,826 out of 33,180,649
Matches: 10,658,608 out of 33,180,649
Mismatches: 5,357,853 out of 33,180,649
Insertions: 359,362 out of 33,180,649
Identity over aligned base-pairs: 65.1%

Block size distribution

Size range All 130,118 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
999
5.0 kb
10 bp - 100 bp
21,290
1.5 Mb
4,942
353.7 kb
100 bp - 1 kb
100,243
32.7 Mb
29,119
11.5 Mb
1 kb - 10 kb
7,521
11.0 Mb
15,750
32.8 Mb
10 kb - 100 kb
54
2.2 Mb
63
1.7 Mb
100 kb - 1 Mb
11
1.4 Mb
17
2.5 Mb