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Arabidopsis thaliana vs Ananas comosus LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Ananas comosus (Ananas comosus, F153) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. 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 thalianaAnanas comosus
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 117,011 alignment blocks

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

Uncovered: 91,541,861 out of 119,667,750
Covered: 28,125,889 out of 119,667,750

Uncovered: 12,956,133 out of 33,775,569
Matches: 13,667,483 out of 33,775,569
Mismatches: 6,735,946 out of 33,775,569
Insertions: 416,007 out of 33,775,569
Identity over aligned base-pairs: 65.6%

Ananas comosus

Uncovered: 288,441,420 out of 315,839,004
Covered: 27,397,584 out of 315,839,004

Uncovered: 10,247,006 out of 27,915,811
Matches: 11,530,697 out of 27,915,811
Mismatches: 5,703,399 out of 27,915,811
Insertions: 434,709 out of 27,915,811
Identity over aligned base-pairs: 65.3%

Block size distribution

Size range All 117,011 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,063
5.7 kb
10 bp - 100 bp
17,962
1.2 Mb
3,404
236.0 kb
100 bp - 1 kb
92,521
30.0 Mb
21,104
8.8 Mb
1 kb - 10 kb
5,465
7.9 Mb
14,065
29.8 Mb
10 kb - 100 kb
32
415.2 kb