Arabidopsis thaliana vs Physcomitrella patens LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Physcomitrella patens (Physcomitrella patens, Phypa_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 thalianaPhyscomitrella patens
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 99,594 alignment blocks

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

Uncovered: 102,984,981 out of 119,667,750
Covered: 16,682,769 out of 119,667,750

Uncovered: 21,129,684 out of 33,775,569
Matches: 8,050,366 out of 33,775,569
Mismatches: 4,359,729 out of 33,775,569
Insertions: 235,790 out of 33,775,569
Identity over aligned base-pairs: 63.7%

Physcomitrella patens

Uncovered: 453,209,731 out of 471,852,792
Covered: 18,643,061 out of 471,852,792

Uncovered: 21,436,115 out of 34,318,961
Matches: 8,249,952 out of 34,318,961
Mismatches: 4,346,640 out of 34,318,961
Insertions: 286,254 out of 34,318,961
Identity over aligned base-pairs: 64.0%

Block size distribution

Size range All 99,594 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
896
4.6 kb
10 bp - 100 bp
20,022
1.4 Mb
2,346
166.1 kb
100 bp - 1 kb
76,014
22.2 Mb
17,488
7.6 Mb
1 kb - 10 kb
2,662
3.6 Mb
9,906
19.2 Mb
10 kb - 100 kb
19
227.9 kb