Arabidopsis thaliana vs Sorghum bicolor LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Sorghum bicolor (Sorghum bicolor, Sorghum_bicolor_NCBIv3) 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: 113,676

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

Uncovered: 93,564,931 out of 119,667,750
Covered: 26,102,819 out of 119,667,750

Uncovered: 14,344,102 out of 33,775,569
Matches: 12,583,906 out of 33,775,569
Mismatches: 6,461,225 out of 33,775,569
Insertions: 386,336 out of 33,775,569

Sorghum bicolor

Uncovered: 679,971,627 out of 708,735,318
Covered: 28,763,691 out of 708,735,318

Uncovered: 19,025,642 out of 39,785,927
Matches: 13,316,654 out of 39,785,927
Mismatches: 6,935,834 out of 39,785,927
Insertions: 507,797 out of 39,785,927

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 Sorghum bicolor
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}