Arabidopsis thaliana vs Prunus avium LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Prunus avium (Prunus avium, PAV_r1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 99. 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 thalianaPrunus avium
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 134,988 alignment blocks

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

Uncovered: 82,742,220 out of 119,667,750
Covered: 36,925,530 out of 119,667,750

Uncovered: 7,901,674 out of 33,775,569
Matches: 17,544,272 out of 33,775,569
Mismatches: 7,797,978 out of 33,775,569
Insertions: 531,645 out of 33,775,569
Identity over aligned base-pairs: 67.8%

Prunus avium

Uncovered: 230,910,175 out of 272,361,615
Covered: 41,451,440 out of 272,361,615

Uncovered: 16,682,088 out of 38,693,511
Matches: 14,740,843 out of 38,693,511
Mismatches: 6,600,778 out of 38,693,511
Insertions: 669,802 out of 38,693,511
Identity over aligned base-pairs: 67.0%

Block size distribution

Size range All 134,988 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,294
7.3 kb
10 bp - 100 bp
19,824
1.3 Mb
4,259
302.1 kb
100 bp - 1 kb
102,139
36.4 Mb
24,920
9.7 Mb
1 kb - 10 kb
11,723
18.1 Mb
15,174
36.8 Mb
10 kb - 100 kb
8
93.8 kb
497
8.9 Mb
100 kb - 1 Mb
1
127.0 kb