BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716293.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,586,734 number of mapped reads = 2,411,558 (93.23%) number of supplementary alignments = 47,790 (1.85%) number of secondary alignments = 0 number of mapped bases = 186,944,949 bp number of sequenced bases = 186,873,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,485 duplication rate = 5.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.483 >>>>>>> ACTG content number of A's = 46,840,509 bp (25.07%) number of C's = 39,061,969 bp (20.9%) number of T's = 55,260,926 bp (29.57%) number of G's = 45,702,083 bp (24.46%) number of N's = 8,081 bp (0%) GC percentage = 45.36% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,237,909 number of insertions = 15,629 mapped reads with insertion percentage = 0.64% number of deletions = 34,171 mapped reads with deletion percentage = 1.39% homopolymer indels = 39% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.4822X There is a 4.68% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 20692865 0.08302031472170335 0.9140231147398105 chr2 243199373 17554090 0.07217983247020954 0.5191598399560703 chr3 198022430 11932168 0.06025664870388673 0.306134208810843 chr4 191154276 9028531 0.04723164550083096 0.41647478055366366 chr5 180915260 9508214 0.05255617464220542 0.2882338450077799 chr6 171115067 11436231 0.0668335711197191 0.34261001964909465 chr7 159138663 11819046 0.07426885319502778 0.68302672606028 chr8 146364022 11819771 0.08075598660441294 0.5164232418865986 chr9 141213431 5619595 0.03979504612418914 0.3418233634756021 chr10 135534747 9596726 0.07080638885908719 0.662402950299945 chr11 135006516 5636291 0.04174828865297139 0.384200285398445 chr12 133851895 6849181 0.05116984709107032 0.2806931152278114 chr13 115169878 3520379 0.030566837971296626 0.21026913290070448 chr14 107349540 3642065 0.03392715981829079 0.2577220088429138 chr15 102531392 3859320 0.037640374569380665 0.2367066602738861 chr16 90354753 5667989 0.06273039117267024 0.3351185743676297 chr17 81195210 4757681 0.05859558710421465 0.33889393736532103 chr18 78077248 5497186 0.07040701537021386 0.5122424443952254 chr19 59128983 4789791 0.0810058072536103 0.6814786512607961 chr20 63025520 5079752 0.08059833540445203 0.3830040905188257 chr21 48129895 3065749 0.06369739638949971 0.40402983288876804 chr22 51304566 3020917 0.05888203011014653 0.3225512647218715 chrMT 16571 121936 7.358397199927584 5.572425047116249 chrX 155270560 11811541 0.07607070522576849 0.36654973616797126 chrY 59373566 617934 0.010407560832711311 0.37736374856187