Caenorhabditis brenneri vs Caenorhabditis elegans LastZ Results

Back to all analyses

Caenorhabditis brenneri (Caenorhabditis brenneri, C_brenneri-6.0.1b) and Caenorhabditis elegans (Caenorhabditis elegans, WBcel235) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release 77. Caenorhabditis brenneri was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 131,050

Genome coverage (bp) Coding exon coverage (bp)
Caenorhabditis brenneri

Uncovered: 130,867,254 out of 190,369,721
Covered: 59,502,467 out of 190,369,721

Uncovered: 11,047,730 out of 36,519,461
Matches: 18,837,561 out of 36,519,461
Mismatches: 6,190,492 out of 36,519,461
Insertions: 443,678 out of 36,519,461

Caenorhabditis elegans

Uncovered: 59,362,178 out of 100,286,401
Covered: 40,924,223 out of 100,286,401

Uncovered: 6,207,498 out of 25,460,976
Matches: 14,302,964 out of 25,460,976
Mismatches: 4,641,698 out of 25,460,976
Insertions: 308,816 out of 25,460,976

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
Other parameters (other)

Chunking parameters

Caenorhabditis brenneri Caenorhabditis elegans
Chunk size 5,000,000 5,000,000
Overlap 10,000 100,000
Group set size 5,000,000 5,000,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}