Oryza sativa Japonica Group vs Chondrus crispus LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Chondrus crispus (Chondrus crispus, ASM35022v2) 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: 9,239

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

Uncovered: 373,084,160 out of 375,049,285
Covered: 1,965,125 out of 375,049,285

Uncovered: 32,825,863 out of 34,403,043
Matches: 990,354 out of 34,403,043
Mismatches: 541,654 out of 34,403,043
Insertions: 45,172 out of 34,403,043

Chondrus crispus

Uncovered: 103,864,766 out of 104,980,420
Covered: 1,115,654 out of 104,980,420

Uncovered: 9,311,410 out of 10,311,317
Matches: 622,177 out of 10,311,317
Mismatches: 349,377 out of 10,311,317
Insertions: 28,353 out of 10,311,317

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 Chondrus crispus
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}