Arabidopsis thaliana vs Brassica rapa LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica rapa (Brassica rapa subsp. pekinensis, IVFCAASv1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 76. 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: 166,096

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

Uncovered: 42,447,937 out of 119,667,750
Covered: 77,219,813 out of 119,667,750

Uncovered: 1,107,650 out of 33,462,323
Matches: 26,646,508 out of 33,462,323
Mismatches: 4,976,833 out of 33,462,323
Insertions: 731,332 out of 33,462,323

Brassica rapa subsp. pekinensis

Uncovered: 214,462,688 out of 283,822,783
Covered: 69,360,095 out of 283,822,783

Uncovered: 20,818,501 out of 48,055,850
Matches: 22,867,270 out of 48,055,850
Mismatches: 3,974,828 out of 48,055,850
Insertions: 395,251 out of 48,055,850

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)