Arabidopsis thaliana vs Theobroma cacao Belizian Criollo B97-61/B2 LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Theobroma cacao Belizian Criollo B97-61/B2 (Theobroma cacao, Criollo_cocoa_genome_V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 104. 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 thalianaTheobroma cacao Belizian Criollo B97-61/B2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 119,520 alignment blocks

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

Uncovered: 82,342,489 out of 119,667,750
Covered: 37,325,261 out of 119,667,750

Uncovered: 7,360,443 out of 33,775,569
Matches: 18,204,380 out of 33,775,569
Mismatches: 7,666,362 out of 33,775,569
Insertions: 544,384 out of 33,775,569
Identity over aligned base-pairs: 68.9%

Theobroma cacao Belizian Criollo B97-61/B2

Uncovered: 288,906,587 out of 324,719,311
Covered: 35,812,724 out of 324,719,311

Uncovered: 6,538,063 out of 29,183,654
Matches: 15,416,922 out of 29,183,654
Mismatches: 6,599,400 out of 29,183,654
Insertions: 629,269 out of 29,183,654
Identity over aligned base-pairs: 68.1%

Block size distribution

Size range All 119,520 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,259
7.0 kb
10 bp - 100 bp
17,240
1.1 Mb
3,006
209.6 kb
100 bp - 1 kb
90,412
32.4 Mb
17,196
6.7 Mb
1 kb - 10 kb
10,609
16.1 Mb
12,382
30.4 Mb
10 kb - 100 kb
461
10.0 Mb
100 kb - 1 Mb
14
2.2 Mb