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Take a look at the resulting file: 61FTVAAXX.ab.sam.links.filtered.sv.txt.

We've highlighted a few lines below:

Code Block
chr_type        SV_type BAL_type        chromosome1     start1-end1     average_dist    chromosome2     start2-end2     nb_pairs        score_strand_filtering  score_order_filtering   score_insert_size_filtering     final_score     breakpoint1_start1-end1 breakpoint2_start2-end2
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INTRA   NORMAL_SENSE    -       chrNC_012967    599566-601025   -       chrNC_012967    663036-664898   430     100%    -       -       1       -       -
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INTRA   NORMAL_SENSE    -       chrNC_012967    3-2025  -       chrNC_012967    4627019-4628998 288     100%    -       -       1       -       -
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INTRA   REVERSE_SENSE   -       chrNC_012967    16999-19033     -       chrNC_012967    2775082-2777014 274     100%    -       -       1       -       -
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titleAny idea what sorts of mutations produced these three structural variants?

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Answers...Answers...

1. This is a tandem head-to-tail duplication of the region from approximately 600000 to 663000.
2. This is just the origin of the circular chromosome, connecting its end to the beginning!
3. This is a big chromosomal inversion mediated by recombination between repeated IS elements in the genome. It would not have been detected if the insert size of the library wasn't > ~1,500 bp!

... Many of the others are due to new insertions of transposable elements.

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