Oryza sativa Japonica vs Sorghum bicolor LastZ Results

Back to all analyses

Oryza sativa Japonica (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 . Oryza sativa Japonica was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 187,234

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: 3,435,785 out of 34,403,043
Matches: 24,108,865 out of 34,403,043
Mismatches: 6,121,750 out of 34,403,043
Insertions: 736,643 out of 34,403,043

Sorghum bicolor

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

Uncovered: 4,387,848 out of 39,785,927
Matches: 27,471,932 out of 39,785,927
Mismatches: 6,961,972 out of 39,785,927
Insertions: 964,175 out of 39,785,927

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Sorghum bicolor
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}