mahulchak
commented
1 year ago Based on the information provided, your initial interpretation seems to be correct (reference has 2 copies of that sequence, but query has one).
On Tue, May 30, 2023, 07:29 LiuShang-777 @.***> wrote:
Hello, I used SVMU for SV detection based on mummer result and found that in the sv.prefix.txt file, the length of CNV in both reference and query genomes were the same like below: REF_CHROM REF_START REF_END SV_TYPE Q_CHROM Q_START Q_END ID LEN COV_REF COV_Q A01 356308 356314 CNV-R A01 245745 245751 0000000023 6 1 2
356314-356308=245751-245745=6, but the covR and covQ are different. Is this means that segments in query have 2 copies in reference genome? I think that (ref_end-ref_start)/(query_end-query_start) should be equal to 2 in this condition.
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LiuShang-777
Hello, I used SVMU for SV detection based on mummer result and found that in the sv.prefix.txt file, the length of CNV in both reference and query genomes were the same like below: REF_CHROM REF_START REF_END SV_TYPE Q_CHROM Q_START Q_END ID LEN COV_REF COV_Q A01 356308 356314 CNV-R A01 245745 245751 0000000023 6 1 2
356314-356308=245751-245745=6, but the covR and covQ are different. Is this means that segments in query have 2 copies in reference genome? I think that (ref_end-ref_start)/(query_end-query_start) should be equal to 2 in this condition.