bwa approximate mapping quality in such way,
{.
.
.
if (p->c1 == 0) return 23;
if (p->c1 > 1) return 0;
if (p->n_mm == mm) return 25;
if (p->c2 == 0) return 37;
n = (p->c2 >= 255)? 255 : p->c2;
return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
}
c1 and c2 are the number of top1 and top2 hits. The higher the mapQ, the lower the probability the read alignment is wrong. I kind of mix up, by above function, if c1 is more than 1, why return the mapQ 0?
Thanks for any comments and answers.
{.
.
.
if (p->c1 == 0) return 23;
if (p->c1 > 1) return 0;
if (p->n_mm == mm) return 25;
if (p->c2 == 0) return 37;
n = (p->c2 >= 255)? 255 : p->c2;
return (23 < g_log_n[n])? 0 : 23 - g_log_n[n];
}
c1 and c2 are the number of top1 and top2 hits. The higher the mapQ, the lower the probability the read alignment is wrong. I kind of mix up, by above function, if c1 is more than 1, why return the mapQ 0?
Thanks for any comments and answers.
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