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Arabidopsis thaliana vs Saccharum spontaneum LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) 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: 447,861

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

Uncovered: 91,977,980 out of 119,667,750
Covered: 27,689,770 out of 119,667,750

Uncovered: 13,745,867 out of 33,775,569
Matches: 12,898,828 out of 33,775,569
Mismatches: 6,688,233 out of 33,775,569
Insertions: 442,641 out of 33,775,569

Saccharum spontaneum

Uncovered: 2,757,487,150 out of 2,900,240,836
Covered: 142,753,686 out of 2,900,240,836

Uncovered: 27,861,097 out of 62,027,027
Matches: 22,052,969 out of 62,027,027
Mismatches: 11,309,592 out of 62,027,027
Insertions: 803,369 out of 62,027,027

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 Saccharum spontaneum
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}