Oryza sativa Japonica Group vs Saccharum spontaneum LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 904,309

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

Uncovered: 291,100,582 out of 375,049,285
Covered: 83,948,703 out of 375,049,285

Uncovered: 3,069,594 out of 34,424,450
Matches: 24,376,952 out of 34,424,450
Mismatches: 6,167,855 out of 34,424,450
Insertions: 810,049 out of 34,424,450

Saccharum spontaneum

Uncovered: 2,495,955,837 out of 2,900,240,836
Covered: 404,284,999 out of 2,900,240,836

Uncovered: 6,904,963 out of 62,027,027
Matches: 43,382,240 out of 62,027,027
Mismatches: 10,412,555 out of 62,027,027
Insertions: 1,327,269 out of 62,027,027

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 Group Saccharum spontaneum
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}