BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080989.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,435,522 number of mapped reads = 2,362,938 (68.78%) number of supplementary alignments = 15,064 (0.44%) number of secondary alignments = 0 number of mapped bases = 148,591,214 bp number of sequenced bases = 148,537,044 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,372 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7958 >>>>>>> ACTG content number of A's = 41,700,378 bp (28.07%) number of C's = 30,877,588 bp (20.79%) number of T's = 42,536,918 bp (28.64%) number of G's = 33,420,187 bp (22.5%) number of N's = 1,973 bp (0%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,130,798 number of insertions = 11,142 mapped reads with insertion percentage = 0.47% number of deletions = 30,799 mapped reads with deletion percentage = 1.29% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.3437X There is a 3.86% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11599031 0.04653561525128557 0.44899828205547854 chr2 243199373 12762109 0.05247591242761962 0.41412551546678894 chr3 198022430 10336349 0.0521978697059722 0.2758692878746279 chr4 191154276 9893894 0.051758685220308645 0.2904405933549136 chr5 180915260 9240585 0.05107686880587077 0.2741384595626066 chr6 171115067 8654796 0.05057880730046992 0.3118605466870649 chr7 159138663 7994689 0.05023725127061046 0.42704913306355924 chr8 146364022 7218250 0.0493171060849913 0.35851610668842737 chr9 141213431 5751965 0.040732421549902004 0.34913605146617244 chr10 135534747 6769715 0.049948187825222416 0.34079042106238516 chr11 135006516 6587066 0.04879072651574832 0.3643489782319862 chr12 133851895 6560262 0.049011349447088515 0.27219319558839605 chr13 115169878 4380219 0.0380326789961521 0.23554276376937847 chr14 107349540 4657220 0.043383697778304406 0.2750646454709529 chr15 102531392 4404331 0.042955927097917485 0.2689508248846877 chr16 90354753 4327650 0.04789620751882306 0.29307765709178907 chr17 81195210 4121973 0.050766208991885116 0.29279253141293393 chr18 78077248 3743815 0.04795014035330753 0.5968488512729441 chr19 59128983 3240428 0.05480270140956086 0.3927018784546812 chr20 63025520 2843790 0.0451212461237924 0.2662202815603321 chr21 48129895 2054339 0.042683222142911384 0.2714433238413572 chr22 51304566 1758768 0.03428092540535281 0.22378199916029323 chrMT 16571 147827 8.920825538591515 5.856734461126851 chrX 155270560 9130130 0.05880142378568094 0.32284580041701844 chrY 59373566 412013 0.0069393339116602835 0.14631209302234316