Medicago truncatula vs Brassica napus LastZ results

Medicago truncatula (Medicago truncatula, MedtrA17_4.0) and Brassica napus (Brassica napus, AST_PRJEB5043_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 truncatulaBrassica napus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 403,390 alignment blocks

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

Uncovered: 355,594,792 out of 412,800,391
Covered: 57,205,599 out of 412,800,391

Uncovered: 19,210,398 out of 50,132,764
Matches: 19,694,652 out of 50,132,764
Mismatches: 10,304,478 out of 50,132,764
Insertions: 923,236 out of 50,132,764
Identity over aligned base-pairs: 63.7%

Brassica napus

Uncovered: 730,521,989 out of 848,200,303
Covered: 117,678,314 out of 848,200,303

Uncovered: 30,305,197 out of 101,157,402
Matches: 47,690,345 out of 101,157,402
Mismatches: 21,687,058 out of 101,157,402
Insertions: 1,474,802 out of 101,157,402
Identity over aligned base-pairs: 67.3%

Block size distribution

Size range All 403,390 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,704
20.2 kb
10 bp - 100 bp
63,575
4.2 Mb
15,806
1.1 Mb
100 bp - 1 kb
311,580
104.1 Mb
90,521
35.3 Mb
1 kb - 10 kb
24,282
38.7 Mb
48,164
106.6 Mb
10 kb - 100 kb
248
6.9 Mb
444
10.1 Mb
100 kb - 1 Mb
1
100.1 kb
8
1.0 Mb