Advantages/Disadvantages of reads mapping on Different contigs?

Question

[sadikhan20084u]

Dear all,

i want to know the advantages/ Disadvantages of Read/Mate mapping on Same and on Different contigs.

for exemple: Contigs Range are:

contig1: 1000-4000; contig2: 4500-5500 contig3: 6000-7000 contig4: 8000-10000

On Same Contig

ReadA 35 abc 1942 37 51M = 4038 97

ReadAMate 177 abc 4038 37 51M = 1942 -97

On Different Contig

ReadC 113 abc 1748 25 51M = 6525 4777

ReadCMate 35 abc 6525 25 51M = 1748 -4777

Anyone can help?

Thanks in advance

[Devon Ryan]

If you know the relative position of the contigs then why don't you make a supercontig and use that for mapping?

[sadikhan20084u]

Obviously i'll make scaffold from this data :) but i want to know the reason of read/mate mapping on same contig and on different contig. and its significance from biological point of view.

[Devon Ryan]

The mates on different contigs are evidence of ordering and distance (or rearrangements/repeats).