Just got the results back from top hap - looked at align summary
Not sure how to read it
Left reads: Input : 25951385 Mapped : 231015 ( 0.9% of input) of these: 114189 (49.4%) have multiple alignments (8625 have >20) Right reads: Input : 25951385 Mapped : 233499 ( 0.9% of input) of these: 111823 (47.9%) have multiple alignments (8625 have >20) 0.9% overall read mapping rate. Aligned pairs: 124107 of these: 85304 (68.7%) have multiple alignments 2055 ( 1.7%) are discordant alignments 0.5% concordant pair alignment rate.
Is this a good. Is this result typical or has the alignment failed. It says only 0.9% mapping rate ( I presume thats a good thing given that only very small proportion of genome is coding).