Arabidopsis thaliana vs Brassica rapa LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Brassica rapa (Brassica rapa, Brapa_1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 70. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

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

Statistics over 166,096 alignment blocks

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
Identity over aligned base-pairs: 82.4%

Brassica rapa

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
Identity over aligned base-pairs: 84.0%