Oryza sativa Japonica Group vs Chlamydomonas reinhardtii LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, Chlamydomonas_reinhardtii_v5.5) 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: 21,592

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

Uncovered: 372,441,909 out of 375,049,285
Covered: 2,607,376 out of 375,049,285

Uncovered: 32,229,621 out of 34,403,043
Matches: 1,458,062 out of 34,403,043
Mismatches: 670,839 out of 34,403,043
Insertions: 44,521 out of 34,403,043

Chlamydomonas reinhardtii

Uncovered: 109,446,095 out of 111,098,438
Covered: 1,652,343 out of 111,098,438

Uncovered: 37,692,140 out of 39,157,072
Matches: 977,248 out of 39,157,072
Mismatches: 451,364 out of 39,157,072
Insertions: 36,320 out of 39,157,072

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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 Chlamydomonas reinhardtii
Chunk size 50,000,000 100,100,000
Overlap 0 100,000
Group set size 0 100,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}