Medicago truncatula vs Oryza sativa Japonica Group LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) 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 truncatulaOryza sativa Japonica Group
Chunk size20,000,00020,100,000
Group set size020,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 147,443 alignment blocks

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

Uncovered: 377,376,360 out of 412,800,391
Covered: 35,424,031 out of 412,800,391

Uncovered: 25,211,565 out of 50,132,764
Matches: 16,070,591 out of 50,132,764
Mismatches: 8,345,660 out of 50,132,764
Insertions: 504,948 out of 50,132,764
Identity over aligned base-pairs: 64.5%

Oryza sativa Japonica Group

Uncovered: 343,863,643 out of 374,424,240
Covered: 30,560,597 out of 374,424,240

Uncovered: 16,015,897 out of 34,124,807
Matches: 11,656,146 out of 34,124,807
Mismatches: 6,058,815 out of 34,124,807
Insertions: 393,949 out of 34,124,807
Identity over aligned base-pairs: 64.4%