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Arabidopsis thaliana vs Arabidopsis lyrata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Arabidopsis lyrata (Arabidopsis lyrata subsp. lyrata, v.1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 90. 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 thalianaArabidopsis lyrata
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 192,580 alignment blocks

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

Uncovered: 25,251,033 out of 119,667,750
Covered: 94,416,717 out of 119,667,750

Uncovered: 587,653 out of 33,775,569
Matches: 30,840,254 out of 33,775,569
Mismatches: 2,113,224 out of 33,775,569
Insertions: 234,438 out of 33,775,569
Identity over aligned base-pairs: 92.9%

Arabidopsis lyrata

Uncovered: 91,565,566 out of 206,667,935
Covered: 115,102,369 out of 206,667,935

Uncovered: 1,189,109 out of 35,389,059
Matches: 31,533,841 out of 35,389,059
Mismatches: 2,402,447 out of 35,389,059
Insertions: 263,662 out of 35,389,059
Identity over aligned base-pairs: 92.2%

Block size distribution

Size range All 192,580 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
2,550
15.9 kb
10 bp - 100 bp
40,038
2.4 Mb
15,724
1.0 Mb
100 bp - 1 kb
117,050
41.9 Mb
53,762
19.1 Mb
1 kb - 10 kb
32,577
82.0 Mb
10,759
23.4 Mb
10 kb - 100 kb
365
4.7 Mb
173
3.3 Mb
100 kb - 1 Mb
18
7.2 Mb
1 Mb - 10 Mb
13
63.4 Mb
10 Mb - 100 Mb
1
13.4 Mb