Arabidopsis thaliana vs Musa acuminata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Musa acuminata (Musa acuminata subsp. malaccensis, ASM31385v1) 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

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Statistics over 92,219 alignment blocks

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

Uncovered: 89,794,366 out of 119,667,750
Covered: 29,873,384 out of 119,667,750

Uncovered: 11,036,499 out of 33,462,323
Matches: 14,782,225 out of 33,462,323
Mismatches: 7,185,985 out of 33,462,323
Insertions: 457,614 out of 33,462,323
Identity over aligned base-pairs: 65.9%

Musa acuminata

Uncovered: 450,483,161 out of 472,960,417
Covered: 22,477,256 out of 472,960,417

Uncovered: 22,753,639 out of 37,920,568
Matches: 10,031,236 out of 37,920,568
Mismatches: 4,790,326 out of 37,920,568
Insertions: 345,367 out of 37,920,568
Identity over aligned base-pairs: 66.1%