Medicago truncatula vs Arabidopsis thaliana LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Medicago truncatula 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)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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterMedicago truncatulaArabidopsis thaliana
Chunk size20,000,00020,100,000
Group set size020,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 160,607 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Medicago truncatula

Uncovered: 365,921,259 out of 412,800,391
Covered: 46,879,132 out of 412,800,391

Uncovered: 18,415,109 out of 50,132,764
Matches: 21,064,131 out of 50,132,764
Mismatches: 9,822,690 out of 50,132,764
Insertions: 830,834 out of 50,132,764
Identity over aligned base-pairs: 66.4%

Arabidopsis thaliana

Uncovered: 83,543,595 out of 119,667,750
Covered: 36,124,155 out of 119,667,750

Uncovered: 8,021,950 out of 33,462,323
Matches: 17,112,580 out of 33,462,323
Mismatches: 7,722,068 out of 33,462,323
Insertions: 605,725 out of 33,462,323
Identity over aligned base-pairs: 67.3%