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Arabidopsis thaliana vs Amborella trichopoda LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Amborella trichopoda (Amborella trichopoda, AMTR1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 94. 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 thalianaAmborella trichopoda
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 116,386 alignment blocks

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

Uncovered: 93,320,892 out of 119,667,750
Covered: 26,346,858 out of 119,667,750

Uncovered: 13,496,593 out of 33,775,569
Matches: 13,325,467 out of 33,775,569
Mismatches: 6,561,294 out of 33,775,569
Insertions: 392,215 out of 33,775,569
Identity over aligned base-pairs: 65.7%

Amborella trichopoda

Uncovered: 682,248,663 out of 706,332,640
Covered: 24,083,977 out of 706,332,640

Uncovered: 10,370,882 out of 25,807,211
Matches: 10,109,768 out of 25,807,211
Mismatches: 4,957,944 out of 25,807,211
Insertions: 368,617 out of 25,807,211
Identity over aligned base-pairs: 65.5%

Block size distribution

Size range All 116,386 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
773
3.8 kb
10 bp - 100 bp
17,869
1.3 Mb
4,414
324.8 kb
100 bp - 1 kb
93,551
28.0 Mb
31,024
11.8 Mb
1 kb - 10 kb
4,189
6.3 Mb
11,967
23.1 Mb
10 kb - 100 kb
4
58.7 kb
27
375.5 kb