BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237607.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,600,051 number of mapped reads = 1,370,671 (85.66%) number of supplementary alignments = 6,977 (0.44%) number of secondary alignments = 0 number of mapped bases = 87,697,999 bp number of sequenced bases = 87,653,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,435 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1013 >>>>>>> ACTG content number of A's = 23,143,868 bp (26.4%) number of C's = 15,769,657 bp (17.99%) number of T's = 27,662,374 bp (31.56%) number of G's = 20,930,869 bp (23.88%) number of N's = 147,109 bp (0.17%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 751,158 number of insertions = 8,058 mapped reads with insertion percentage = 0.58% number of deletions = 26,314 mapped reads with deletion percentage = 1.9% homopolymer indels = 45.62% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.2972X There is a 2.57% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 6631118 0.02660421857083357 0.357216698523822 chr2 243199373 7269918 0.02989283200166803 0.561031560145647 chr3 198022430 5870273 0.02964448522321436 0.18603027016174326 chr4 191154276 5765093 0.03015937242230459 0.19581241903381036 chr5 180915260 5418785 0.02995206153422326 0.1884387754023058 chr6 171115067 5344282 0.031232094833589377 0.2852710250542012 chr7 159138663 5510770 0.03462873129705758 0.3749855329486658 chr8 146364022 4019109 0.027459678581393452 0.2881621696967763 chr9 141213431 3886004 0.027518657201948446 0.30217154224118153 chr10 135534747 4280799 0.03158451315809074 0.24852003570014117 chr11 135006516 4101881 0.030382837225426958 0.26709938969517993 chr12 133851895 3172391 0.023700755226513603 0.17627894323746154 chr13 115169878 2729603 0.023700667634639676 0.17487219088362438 chr14 107349540 2654849 0.024730883802576147 0.19335868980561724 chr15 102531392 2378790 0.02320060182153774 0.17119594356649132 chr16 90354753 2313787 0.02560780615492358 0.22258774177161578 chr17 81195210 2204795 0.02715424961644905 0.19771914017752468 chr18 78077248 2188214 0.028026269573435784 0.5347248779539059 chr19 59128983 1949221 0.032965576289380794 0.3042598637595214 chr20 63025520 1676912 0.026606872898470333 0.18173755624063684 chr21 48129895 1224642 0.025444518422489806 0.18813026225607773 chr22 51304566 1043654 0.02034232196799014 0.15319661186471542 chrMT 16571 9225 0.5566954317784081 0.9143458269483772 chrX 155270560 5799008 0.03734776251209502 0.24425819078752445 chrY 59373566 254876 0.004292752097793823 0.09884363170675466