Hi there. I've been using breakdancer recently. And here is an example of my output.

chrM    6240       17+17-  chrM    7310       17+17-  INS     -248    99      7       bam|7      NA
chrM    7712       7+12-   chrM    8606       7+12-   INS     -265    40      2       bam|2      NA
chr1    869287     2+0-    chr1    870349     0+2-    DEL     814     90      2       bam|2      NA
chr1    953405     2+2-    chr1    953584     2+2-    INS     -148    56      2       bam|2      NA
chr1    963921     3+0-    chr1    964569     0+3-    DEL     435     99      3       bam|3      0.35
chr1    1127799    4+4-    chr1    1128239    4+4-    INS     -99     87      4       bam|4      NA
chr1    1131115    3+3-    chr1    1131373    3+3-    INS     -221    74      3       bam|3      NA
chr1    1161728    5+0-    chr1    1161973    0+5-    DEL     65      99      5       bam|5      1.05

Question 1 : The last column is estimated copy number. What does NA mean?

Question 2 : Column 2 and 5 are position1 and position2. I know breakdancer only examines read pairs spanning events and Column 8--size may be not equal to position2 - position1. But some estimated sizes is far less than position2-position1. Is this alright ?

Thank you very much for helping me.