Arabidopsis thaliana vs Chlamydomonas reinhardtii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Chlamydomonas reinhardtii (Chlamydomonas reinhardtii, v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 13,573

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 117,999,755 out of 119,667,750
Covered: 1,667,995 out of 119,667,750

Uncovered: 32,226,032 out of 33,775,569
Matches: 1,020,997 out of 33,775,569
Mismatches: 515,232 out of 33,775,569
Insertions: 13,308 out of 33,775,569

Chlamydomonas reinhardtii

Uncovered: 119,391,534 out of 120,404,952
Covered: 1,013,418 out of 120,404,952

Uncovered: 18,782,505 out of 19,667,536
Matches: 580,706 out of 19,667,536
Mismatches: 295,869 out of 19,667,536
Insertions: 8,456 out of 19,667,536

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

Arabidopsis thaliana Chlamydomonas reinhardtii
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}