Tophat mapibility over 100%

[zack80]

I am running tophat on my paired samples. However, I got a mappability over 100 %. Is that possible??? Am I missing sth ?

Thanks!

[Tue Nov 13 13:03:09 2012] Beginning TopHat run (v1.4.1)
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[Tue Nov 13 13:03:09 2012] Preparing output location ./Results/***/tophat/
[Tue Nov 13 13:03:13 2012] Checking for Bowtie index files
[Tue Nov 13 13:03:13 2012] Checking for reference FASTA file
[Tue Nov 13 13:03:14 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 13 13:03:14 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Nov 13 13:03:14 2012] Generating SAM header for /nfs/nfs_wooi/mm9_hyojin/mm9
format: fastq
quality scale: phred33 (default)
[Tue Nov 13 13:06:58 2012] Reading known junctions from GTF file
[Tue Nov 13 13:07:15 2012] Preparing reads
left reads: min. length=81, count=70470512
right reads: min. length=81, count=70417033
[Tue Nov 13 14:31:38 2012] Creating transcriptome data files..
[Tue Nov 13 15:12:24 2012] Building Bowtie index from ucsc_ensGene.fa
[Tue Nov 13 15:31:51 2012] Mapping left_kept_reads against transcriptome ucsc_ensGene with Bowtie
[Tue Nov 13 17:05:14 2012] Mapping right_kept_reads against transcriptome ucsc_ensGene with Bowtie
[Tue Nov 13 19:51:49 2012] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[Tue Nov 13 21:14:31 2012] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[Tue Nov 13 22:14:58 2012] Resuming TopHat pipeline with unmapped reads
[Tue Nov 13 22:14:58 2012] Mapping left_kept_reads.m2g_um against mm9 with Bowtie
[Tue Nov 13 23:40:50 2012] Processing bowtie hits
[Wed Nov 14 00:50:27 2012] Mapping left_kept_reads.m2g_um_seg1 against mm9 with Bowtie (1/3)
[Wed Nov 14 01:03:40 2012] Mapping left_kept_reads.m2g_um_seg2 against mm9 with Bowtie (2/3)
[Wed Nov 14 01:17:33 2012] Mapping left_kept_reads.m2g_um_seg3 against mm9 with Bowtie (3/3)
[Wed Nov 14 01:29:25 2012] Mapping right_kept_reads.m2g_um against mm9 with Bowtie
[Wed Nov 14 02:26:56 2012] Processing bowtie hits
[Wed Nov 14 03:40:40 2012] Mapping right_kept_reads.m2g_um_seg1 against mm9 with Bowtie (1/3)
[Wed Nov 14 04:14:04 2012] Mapping right_kept_reads.m2g_um_seg2 against mm9 with Bowtie (2/3)
[Wed Nov 14 04:46:41 2012] Mapping right_kept_reads.m2g_um_seg3 against mm9 with Bowtie (3/3)
[Wed Nov 14 05:03:45 2012] Searching for junctions via segment mapping
[Wed Nov 14 07:20:04 2012] Retrieving sequences for splices
[Wed Nov 14 07:48:20 2012] Indexing splices
[Wed Nov 14 08:05:47 2012] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie (1/3)
[Wed Nov 14 08:13:28 2012] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie (2/3)
[Wed Nov 14 08:19:10 2012] Mapping left_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie (3/3)
[Wed Nov 14 08:22:04 2012] Joining segment hits
[Wed Nov 14 09:16:08 2012] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie (1/3)
[Wed Nov 14 09:20:51 2012] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie (2/3)
[Wed Nov 14 09:25:46 2012] Mapping right_kept_reads.m2g_um_seg3 against segment_juncs with Bowtie (3/3)
[Wed Nov 14 09:30:10 2012] Joining segment hits
[Wed Nov 14 10:18:23 2012] Reporting output tracks
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Run complete [23:33:25 elapsed]

Wed Nov 14 12:36:34 CST 2012 Compute Statistics........
Original read (mate 1 and mate 2): 141352022
Total mapped reads : 154111182
Mappability (%) : 109.027