Medicago truncatula vs Malus domestica Golden LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Malus domestica Golden (Malus domestica, ASM211411v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 101. 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

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

Chunking parameters

ParameterMedicago truncatulaMalus domestica Golden
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 275,664 alignment blocks

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

Uncovered: 352,702,896 out of 412,800,391
Covered: 60,097,495 out of 412,800,391

Uncovered: 14,865,978 out of 50,132,764
Matches: 24,254,101 out of 50,132,764
Mismatches: 10,245,698 out of 50,132,764
Insertions: 766,987 out of 50,132,764
Identity over aligned base-pairs: 68.8%

Malus domestica Golden

Uncovered: 626,043,639 out of 702,961,352
Covered: 76,917,713 out of 702,961,352

Uncovered: 9,052,038 out of 47,560,911
Matches: 26,755,543 out of 47,560,911
Mismatches: 10,778,846 out of 47,560,911
Insertions: 974,484 out of 47,560,911
Identity over aligned base-pairs: 69.5%

Block size distribution

Size range All 275,664 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,858
14.6 kb
10 bp - 100 bp
45,235
3.0 Mb
13,338
962.4 kb
100 bp - 1 kb
207,763
69.4 Mb
65,247
22.3 Mb
1 kb - 10 kb
19,654
31.3 Mb
24,761
61.1 Mb
10 kb - 100 kb
154
3.5 Mb
937
20.0 Mb
100 kb - 1 Mb
18
2.8 Mb