Midas cichlid vs Zebrafish LastZ results

Midas cichlid (Amphilophus citrinellus, Midas_v5) and Zebrafish (Danio rerio, GRCz11) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 94. Midas cichlid 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

ParameterMidas cichlidZebrafish
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options

Statistics over 308,844 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Midas cichlid

Uncovered: 783,537,510 out of 844,902,565
Covered: 61,365,055 out of 844,902,565

Uncovered: 5,694,189 out of 34,548,519
Matches: 20,663,549 out of 34,548,519
Mismatches: 7,636,604 out of 34,548,519
Insertions: 554,177 out of 34,548,519
Identity over aligned base-pairs: 71.6%

Zebrafish

Uncovered: 1,309,770,487 out of 1,373,471,384
Covered: 63,700,897 out of 1,373,471,384

Uncovered: 9,423,360 out of 42,031,845
Matches: 23,081,085 out of 42,031,845
Mismatches: 9,060,070 out of 42,031,845
Insertions: 467,330 out of 42,031,845
Identity over aligned base-pairs: 70.8%

Block size distribution

Size range All 308,844 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,896
8.5 kb
10 bp - 100 bp
46,046
3.3 Mb
14,597
1.1 Mb
100 bp - 1 kb
254,053
63.3 Mb
78,465
24.5 Mb
1 kb - 10 kb
6,828
11.4 Mb
15,244
37.3 Mb
10 kb - 100 kb
21
313.8 kb
695
13.8 Mb
100 kb - 1 Mb
13
1.8 Mb