Arabidopsis thaliana vs Helianthus annuus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Helianthus annuus (Helianthus annuus, HanXRQr1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 91. 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

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

ParameterArabidopsis thalianaHelianthus annuus
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 240,077 alignment blocks

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

Uncovered: 84,324,102 out of 119,667,750
Covered: 35,343,648 out of 119,667,750

Uncovered: 9,589,180 out of 33,775,569
Matches: 15,747,468 out of 33,775,569
Mismatches: 7,739,306 out of 33,775,569
Insertions: 699,615 out of 33,775,569
Identity over aligned base-pairs: 65.1%

Helianthus annuus

Uncovered: 2,956,783,382 out of 3,027,844,945
Covered: 71,061,563 out of 3,027,844,945

Uncovered: 18,241,125 out of 54,343,734
Matches: 23,980,309 out of 54,343,734
Mismatches: 11,337,645 out of 54,343,734
Insertions: 784,655 out of 54,343,734
Identity over aligned base-pairs: 66.4%

Block size distribution

Size range All 240,077 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,514
8.3 kb
10 bp - 100 bp
39,108
2.7 Mb
15,149
1.1 Mb
100 bp - 1 kb
184,786
61.6 Mb
74,764
27.1 Mb
1 kb - 10 kb
14,593
22.5 Mb
27,479
57.6 Mb
10 kb - 100 kb
76
789.8 kb
137
1.8 Mb