BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237866.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 = 3,689,431 number of mapped reads = 3,023,468 (81.95%) number of supplementary alignments = 20,200 (0.55%) number of secondary alignments = 0 number of mapped bases = 199,152,546 bp number of sequenced bases = 199,068,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,664 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.615 >>>>>>> ACTG content number of A's = 55,857,069 bp (28.06%) number of C's = 37,818,076 bp (19%) number of T's = 62,403,155 bp (31.35%) number of G's = 42,953,114 bp (21.58%) number of N's = 37,048 bp (0.02%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,730,997 number of insertions = 17,218 mapped reads with insertion percentage = 0.56% number of deletions = 50,817 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.0643X std coverageData = 0.5754X There is a 5.6% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 13412431 0.053811023403628755 0.9643299946024646 chr2 243199373 16948325 0.06968901601567863 0.7211002367297922 chr3 198022430 12927207 0.06528152896618833 0.2868104852235067 chr4 191154276 13830796 0.0723541020866308 0.3484251908340456 chr5 180915260 11179908 0.061796379144578514 0.2806201310089462 chr6 171115067 12584681 0.07354513673538754 0.4361267340215631 chr7 159138663 11100305 0.06975240831324567 0.7757379799973512 chr8 146364022 12066029 0.08243849024591576 0.689060178540934 chr9 141213431 8499377 0.060188162980049684 0.6050491755153227 chr10 135534747 9797742 0.07228952144648192 0.6408438811171868 chr11 135006516 8945159 0.06625723902096696 0.5635930828093535 chr12 133851895 9643386 0.07204519592344957 0.30931036317426314 chr13 115169878 7347783 0.06379952056561178 0.2753448555044992 chr14 107349540 5990266 0.05580150599620641 0.37153128979702904 chr15 102531392 4969911 0.04847209135715235 0.24406431038099202 chr16 90354753 5458654 0.060413578907132864 0.3762395012681299 chr17 81195210 5087550 0.06265825286984293 0.3892291215762541 chr18 78077248 5740746 0.07352649007301076 1.2237923772094759 chr19 59128983 3732954 0.06313238974531322 0.7638444282929386 chr20 63025520 3889129 0.06170721003174587 0.3079170113505135 chr21 48129895 2730167 0.0567249731170201 0.3277342506053761 chr22 51304566 1793849 0.03496470470094221 0.20304659665845862 chrMT 16571 51377 3.1004163900790536 2.4980654669632765 chrX 155270560 10848463 0.06986812567688298 0.42758205876462874 chrY 59373566 576351 0.009707198654700983 0.24316890147984443