cornetto

asmstats output

Output will be as follows

Definition: A contig will taken to belong to a chromosome if classified so by minidotplot script above (cornetto fixasm, 50% of its length is actually aligned to the chromosome).

1. Contigs containing one or more telomeres at the end:

Using belonging contigs, a table with 4 columns below will created, with one row per each chromosome on the reference. - chr: chromosome - T2T?: y for two telomeres at the ends, `n otherwise. Comma separated chr per each contig belonging to the chromosome - NTelo: total number of telomeres in contigs belonging to the chromosome - Telocontiglen: comma separated contig lengths

1. Contigs whose majority is mapped to the corresponding chromosome

Using belonging contigs, a table with following columns will be created, with one row per each chromosome on the reference. - chr: chromosome - Ncontigsofsize>=KMbasealignedtochr: Number of contigs of size >= K Mbase aligned to the chr - %ofchrsequencecoveredbycontigsofsize>=KMbase: Pecentage of the chromosome sequence covered by contigs of size >= K Mbase

K values are 0Mbase, 0.1Mbase, 1Mbase, 5Mbase and 10Mbase

1. LX of Contigs whose majority is mapped to the corresponding chromosome

Using belonging contigs, a table with following columns will be created, with one row per each chromosome on the reference.

• chr: chromosome
• L50: Min N major-mapping contigs that cover >= 50% of chromosome [n=X]
• L90: Min N major-mapping contigs that cover >= 90% of chromosome [n=X]
• L95: Min N major-mapping contigs that cover >= 95% of chromosome [n=X]
• L99: Min N major-mapping contigs that cover >= 99% of chromosome [n=X]
• CumCovN5: Cumulative % covered by n=5 largest contigs [n%,n%,n%,n%,n%]

1. Contigs whose majority is mapped to another chromosome

Using non-belonging contigs, a table with following columns will be created, with one row per each chromosome on the reference. - chr: chromosome - Ncontigsofsize>=KMbasealignedtochr: Number of contigs of size >= K Mbase aligned to the chr - %ofchrsequencecoveredbycontigsofsize>=KMbase: Pecentage of the chromosome sequence covered by contigs of size >= K Mbase

This site is open source. Improve this page.