BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975195.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 5,818,800 number of mapped reads = 5,632,585 (96.8%) number of supplementary alignments = 82,228 (1.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,817,818 number of mapped paired reads (second in pair) = 2,814,767 number of mapped paired reads (both in pair) = 5,584,870 number of mapped paired reads (singletons) = 47,715 number of mapped bases = 761,330,645 bp number of sequenced bases = 760,741,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,181,207 duplication rate = 18.3% >>>>>>> Insert size mean insert size = 104,755.8799 std insert size = 3,094,971.5826 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 53.4062 >>>>>>> ACTG content number of A's = 224,733,769 bp (29.54%) number of C's = 152,125,319 bp (20%) number of T's = 224,598,968 bp (29.52%) number of G's = 159,205,175 bp (20.93%) number of N's = 77,882 bp (0.01%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 9,500,992 number of insertions = 156,899 mapped reads with insertion percentage = 2.63% number of deletions = 295,761 mapped reads with deletion percentage = 5.04% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.2459X std coverageData = 4.6843X There is a 11.59% of reference with a coverageData >= 1X There is a 7% of reference with a coverageData >= 2X There is a 2.18% of reference with a coverageData >= 3X There is a 1.24% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 76206878 0.30574398448539875 5.849736867766203 chr2 243199373 53429855 0.21969569387006602 3.413533518123567 chr3 198022430 55744302 0.2815049891065371 1.0865132827998751 chr4 191154276 42365095 0.22162776520887245 2.6443317484945084 chr5 180915260 66144936 0.36561280679142266 0.998669461501103 chr6 171115067 37650166 0.22002835086404168 1.5940773027769024 chr7 159138663 32401343 0.20360446914148073 1.963993507927827 chr8 146364022 48630696 0.33225853823557816 1.5212532587467467 chr9 141213431 26826284 0.189969777024963 4.573425495592924 chr10 135534747 42034843 0.3101407124772218 17.626234919803675 chr11 135006516 29159188 0.21598356037867092 2.147644917816811 chr12 133851895 26954911 0.2013786282218866 0.7077904731658619 chr13 115169878 15341658 0.1332089454848602 0.5576716348193931 chr14 107349540 21928529 0.20427222138073436 0.762967835051638 chr15 102531392 16957766 0.16539096631010336 0.6284717601733826 chr16 90354753 23599563 0.2611878425476964 5.83446022754656 chr17 81195210 12986392 0.15994037086670507 2.5391958583494905 chr18 78077248 18161007 0.23260306254646682 4.5501862018642765 chr19 59128983 10981229 0.1857165207796657 2.699362435621645 chr20 63025520 11828167 0.18767266021763881 1.0473889161884358 chr21 48129895 8666614 0.18006717031067698 1.4974121974705115 chr22 51304566 6009736 0.11713842389778718 0.5584093964895042 chrMT 16571 148619 8.968619878100295 5.605754123714201 chrX 155270560 73834710 0.4755229194768152 1.8866401483819966 chrY 59373566 3338158 0.056222966294461746 4.341909335496855