minimap2 on ref sequences with high similarity

[liuqianhn]

Hi Heng and team,

I recently used minimap2 on a set of reference sequences whose sequence similarity might be high. I got abnormal percentage of singletons (-326.79% are singletons as shown below). Could you please kindly advise whether this will affect the mapping quality a lot? Thanks.

[M::mm_idx_stat::3158.808*1.64] distinct minimizers: 324292167 (-326.79% are singletons); average occurrences: 37.971; average spacing: 6.003; total length: 73917264088