Arabidopsis thaliana vs Populus trichocarpa LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Populus trichocarpa (Populus trichocarpa, Pop_tri_v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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)3000
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 thalianaPopulus trichocarpa
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 170,320 alignment blocks

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

Uncovered: 82,241,839 out of 119,667,750
Covered: 37,425,911 out of 119,667,750

Uncovered: 7,617,335 out of 33,775,569
Matches: 17,852,111 out of 33,775,569
Mismatches: 7,727,402 out of 33,775,569
Insertions: 578,721 out of 33,775,569
Identity over aligned base-pairs: 68.2%

Populus trichocarpa

Uncovered: 379,926,240 out of 434,132,815
Covered: 54,206,575 out of 434,132,815

Uncovered: 12,378,467 out of 48,383,886
Matches: 24,339,052 out of 48,383,886
Mismatches: 10,618,869 out of 48,383,886
Insertions: 1,047,498 out of 48,383,886
Identity over aligned base-pairs: 67.6%

Block size distribution

Size range All 170,320 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,805
9.8 kb
10 bp - 100 bp
24,868
1.6 Mb
4,726
330.5 kb
100 bp - 1 kb
129,619
46.0 Mb
26,910
10.6 Mb
1 kb - 10 kb
14,028
21.0 Mb
19,241
47.5 Mb
10 kb - 100 kb
562
9.9 Mb
100 kb - 1 Mb
2
234.5 kb