Upcoming Ensembl Platform Transition

This is the final release of its kind on this website.

In summer 2026, this site will bring you to the new Ensembl platform currently at beta.ensembl.org.
Please bookmark this archive to retain access to the current site, tools and functionality until they are available on the new platform -> eg63-plants.ensembl.org

Ensembl Genomes HomeEnsembl Plants HomeEnsembl Plants Home ▼
More ▼
Search »

Oryza sativa Japonica Group vs Sorghum bicolor LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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 GroupSorghum bicolor
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 187,234 alignment blocks

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

Uncovered: 298,485,504 out of 375,049,285
Covered: 76,563,781 out of 375,049,285

Uncovered: 3,441,925 out of 34,818,902
Matches: 24,429,972 out of 34,818,902
Mismatches: 6,202,108 out of 34,818,902
Insertions: 744,897 out of 34,818,902
Identity over aligned base-pairs: 77.9%

Sorghum bicolor

Uncovered: 632,655,992 out of 708,735,318
Covered: 76,079,326 out of 708,735,318

Uncovered: 4,387,986 out of 39,785,927
Matches: 27,471,419 out of 39,785,927
Mismatches: 6,962,254 out of 39,785,927
Insertions: 964,268 out of 39,785,927
Identity over aligned base-pairs: 77.6%

Block size distribution

Size range All 187,234 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,621
9.0 kb
10 bp - 100 bp
26,726
1.7 Mb
9,852
692.0 kb
100 bp - 1 kb
130,787
49.7 Mb
44,546
14.9 Mb
1 kb - 10 kb
28,092
48.4 Mb
13,275
31.2 Mb
10 kb - 100 kb
8
85.1 kb
303
6.1 Mb
100 kb - 1 Mb
17
8.5 Mb
1 Mb - 10 Mb
12
38.5 Mb