Oryza sativa Japonica Group vs Brassica napus LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) 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: 311,135

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

Uncovered: 337,406,533 out of 375,049,285
Covered: 37,642,752 out of 375,049,285

Uncovered: 14,357,048 out of 34,403,043
Matches: 12,474,343 out of 34,403,043
Mismatches: 6,954,670 out of 34,403,043
Insertions: 616,982 out of 34,403,043

Brassica napus

Uncovered: 761,084,360 out of 848,200,303
Covered: 87,115,943 out of 848,200,303

Uncovered: 43,320,793 out of 101,157,402
Matches: 38,081,154 out of 101,157,402
Mismatches: 18,702,347 out of 101,157,402
Insertions: 1,053,108 out of 101,157,402

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 Brassica napus
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}