Oryza sativa Japonica vs Chlamydomonas reinhardtii LastZ Results

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Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 17,708

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

Uncovered: 371,894,138 out of 374,424,240
Covered: 2,530,102 out of 374,424,240

Uncovered: 32,142,092 out of 34,124,807
Matches: 1,338,952 out of 34,124,807
Mismatches: 605,800 out of 34,124,807
Insertions: 37,963 out of 34,124,807

Chlamydomonas reinhardtii

Uncovered: 119,091,354 out of 120,404,952
Covered: 1,313,598 out of 120,404,952

Uncovered: 18,626,415 out of 19,668,972
Matches: 698,756 out of 19,668,972
Mismatches: 323,720 out of 19,668,972
Insertions: 20,081 out of 19,668,972

Configuration parameters

ParameterValue
Gap open penalty (O)
Gap extend penalty (E)
HSP threshold (K)
Threshold for gapped extension (L)
Threshold for alignments between gapped alignment blocks (H)
Masking count (M)
Seed and Transition value (T)
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)