Just wondering if anybody can help me to understand the following example:

ref: AC GTACGT

r1 : ACCGTACGT

r2 : AC......T

Will the CIGARs be:

2M1I6M

2M6N1M

OR will it be:

2M1I6M

2M5N1M

In other words, if there are alignment positions with possible insertions in the reference, will the skipped positions (Ns) take into account these possible insertions?

Also, how do mappers determine segments with skipped N positions?

Thanks!

ref: AC GTACGT

r1 : ACCGTACGT

r2 : AC......T

Will the CIGARs be:

2M1I6M

2M6N1M

OR will it be:

2M1I6M

2M5N1M

In other words, if there are alignment positions with possible insertions in the reference, will the skipped positions (Ns) take into account these possible insertions?

Also, how do mappers determine segments with skipped N positions?

Thanks!

## Comment