Arabidopsis thaliana vs Saccharum spontaneum LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Saccharum spontaneum (Saccharum spontaneum, Sspon.HiC_chr_asm) 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 thalianaSaccharum spontaneum
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 447,861 alignment blocks

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

Uncovered: 91,977,980 out of 119,667,750
Covered: 27,689,770 out of 119,667,750

Uncovered: 13,745,867 out of 33,775,569
Matches: 12,898,828 out of 33,775,569
Mismatches: 6,688,233 out of 33,775,569
Insertions: 442,641 out of 33,775,569
Identity over aligned base-pairs: 64.4%

Saccharum spontaneum

Uncovered: 2,757,487,150 out of 2,900,240,836
Covered: 142,753,686 out of 2,900,240,836

Uncovered: 27,861,097 out of 62,027,027
Matches: 22,052,969 out of 62,027,027
Mismatches: 11,309,592 out of 62,027,027
Insertions: 803,369 out of 62,027,027
Identity over aligned base-pairs: 64.5%

Block size distribution

Size range All 447,861 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,160
16.3 kb
10 bp - 100 bp
69,497
4.8 Mb
15,843
1.2 Mb
100 bp - 1 kb
348,946
115.7 Mb
109,160
44.6 Mb
1 kb - 10 kb
26,258
38.2 Mb
57,353
112.4 Mb
10 kb - 100 kb
53
666.8 kb