BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506329.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 6,909,341 number of mapped reads = 4,496,998 (65.09%) number of supplementary alignments = 59,865 (0.87%) number of secondary alignments = 0 number of mapped bases = 352,076,670 bp number of sequenced bases = 351,927,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 783,647 duplication rate = 12.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1168 >>>>>>> ACTG content number of A's = 99,088,488 bp (28.16%) number of C's = 63,391,703 bp (18.01%) number of T's = 97,230,021 bp (27.63%) number of G's = 92,140,011 bp (26.18%) number of N's = 77,480 bp (0.02%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,789,717 number of insertions = 28,696 mapped reads with insertion percentage = 0.62% number of deletions = 73,764 mapped reads with deletion percentage = 1.61% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 0.1137X std coverageData = 0.7521X There is a 6.8% of reference with a coverageData >= 1X There is a 2.35% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.46% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 25210159 0.10114381620738269 1.0490305676278404 chr2 243199373 25252078 0.1038328252597921 0.8217367859292012 chr3 198022430 21573228 0.10894335555825671 0.5149351687850714 chr4 191154276 21943538 0.11479491047325564 0.738884362647388 chr5 180915260 26721466 0.14770155928250608 0.6154125917155641 chr6 171115067 13959959 0.08158228988683972 0.4776245394104872 chr7 159138663 18168000 0.1141645886518476 0.8108177031868006 chr8 146364022 19378047 0.1323962455746126 1.1257993137932767 chr9 141213431 8506501 0.06023861143916261 0.65727316528504 chr10 135534747 19662870 0.1450762290499572 0.8665157022455493 chr11 135006516 15128750 0.11205940608081465 0.7503923452595299 chr12 133851895 15015140 0.11217726876410677 0.5464893315421493 chr13 115169878 7727566 0.06709711023571632 0.40148236342813803 chr14 107349540 11054346 0.10297525261868845 0.5366240716520886 chr15 102531392 12584877 0.12274169651378575 0.5712670890317418 chr16 90354753 14066085 0.15567620443829888 0.7821939621142221 chr17 81195210 10725205 0.13209159752157792 0.660507500690173 chr18 78077248 7138405 0.09142746680825635 0.8958046620618155 chr19 59128983 10367425 0.17533575708548885 0.9876280223577105 chr20 63025520 10260022 0.16279154856635852 0.690776026654665 chr21 48129895 6471390 0.134456765384591 0.7215536629533493 chr22 51304566 4885726 0.09522984757341091 0.5132608830390328 chrMT 16571 97738 5.898135296602498 5.424309863072685 chrX 155270560 24797280 0.15970368110992839 0.6845770393733965 chrY 59373566 1380869 0.023257302753215126 0.8197581399163459