BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617552.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 53,049,146 number of mapped reads = 52,421,879 (98.82%) number of supplementary alignments = 1,461,408 (2.75%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,386,945 number of mapped paired reads (second in pair) = 26,034,934 number of mapped paired reads (both in pair) = 51,992,466 number of mapped paired reads (singletons) = 429,413 number of mapped bases = 6,982,907,468 bp number of sequenced bases = 6,977,734,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,182,169 duplication rate = 25.48% >>>>>>> Insert size mean insert size = 169,832.4129 std insert size = 3,941,558.5118 median insert size = 272 >>>>>>> Mapping quality mean mapping quality = 53.4378 >>>>>>> ACTG content number of A's = 2,025,211,564 bp (29.02%) number of C's = 1,313,500,922 bp (18.82%) number of T's = 2,103,319,819 bp (30.14%) number of G's = 1,535,419,537 bp (22%) number of N's = 282,591 bp (0%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 77,657,788 number of insertions = 1,250,442 mapped reads with insertion percentage = 2.23% number of deletions = 2,594,740 mapped reads with deletion percentage = 4.75% homopolymer indels = 46.18% >>>>>>> Coverage mean coverageData = 2.2557X std coverageData = 25.2633X There is a 44.1% of reference with a coverageData >= 1X There is a 32.69% of reference with a coverageData >= 2X There is a 24.73% of reference with a coverageData >= 3X There is a 19.37% of reference with a coverageData >= 4X There is a 15.32% of reference with a coverageData >= 5X There is a 12.32% of reference with a coverageData >= 6X There is a 9.99% of reference with a coverageData >= 7X There is a 8.18% of reference with a coverageData >= 8X There is a 6.74% of reference with a coverageData >= 9X There is a 5.59% of reference with a coverageData >= 10X There is a 4.67% of reference with a coverageData >= 11X There is a 3.92% of reference with a coverageData >= 12X There is a 3.3% of reference with a coverageData >= 13X There is a 2.8% of reference with a coverageData >= 14X There is a 2.38% of reference with a coverageData >= 15X There is a 2.04% of reference with a coverageData >= 16X There is a 1.75% of reference with a coverageData >= 17X There is a 1.5% of reference with a coverageData >= 18X There is a 1.3% of reference with a coverageData >= 19X There is a 1.13% of reference with a coverageData >= 20X There is a 0.98% of reference with a coverageData >= 21X There is a 0.85% of reference with a coverageData >= 22X There is a 0.75% of reference with a coverageData >= 23X There is a 0.66% of reference with a coverageData >= 24X There is a 0.58% of reference with a coverageData >= 25X There is a 0.51% of reference with a coverageData >= 26X There is a 0.45% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.36% of reference with a coverageData >= 29X There is a 0.32% of reference with a coverageData >= 30X There is a 0.29% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 541835946 2.1738599640239213 21.388935359370258 chr2 243199373 648598310 2.66694071616706 35.897714540015606 chr3 198022430 407695325 2.0588340674336743 4.2119894182867865 chr4 191154276 439068854 2.2969345137746227 27.559049332277027 chr5 180915260 478605935 2.6454702328592954 5.595532189979127 chr6 171115067 409454835 2.3928625466978897 18.02800488512211 chr7 159138663 371536593 2.334672077771572 30.989005884818837 chr8 146364022 360356156 2.4620542061900976 7.515018580841049 chr9 141213431 396274944 2.806212845292315 53.836762699881874 chr10 135534747 388404683 2.86572035287748 49.36011042007364 chr11 135006516 345325484 2.5578430895883573 15.681402066470278 chr12 133851895 303793170 2.2696217337827007 10.082763426031837 chr13 115169878 198436939 1.7229933941581497 3.8577488152424277 chr14 107349540 208131050 1.9388164122547706 5.002147042313793 chr15 102531392 130350891 1.2713266489154853 5.07718600348158 chr16 90354753 229491100 2.539889628163778 38.726100722096575 chr17 81195210 107983026 1.3299186737739825 14.058888258966519 chr18 78077248 213455368 2.733899739908866 36.06581160057127 chr19 59128983 81760548 1.3827490995405756 13.04226242120791 chr20 63025520 192975658 3.0618653840539514 9.909284280817088 chr21 48129895 85533254 1.777133608955515 11.901760150121637 chr22 51304566 42114694 0.8208761380029995 3.355295650322863 chrMT 16571 2359971 142.4157262687828 71.28551877221089 chrX 155270560 292901226 1.8863925395773673 7.955756910753738 chrY 59373566 106463508 1.7931129149291791 40.265802866866466