BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230394.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 = 2,818,103 number of mapped reads = 2,492,016 (88.43%) number of supplementary alignments = 19,827 (0.7%) number of secondary alignments = 0 number of mapped bases = 161,475,529 bp number of sequenced bases = 161,395,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,124 duplication rate = 4.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3349 >>>>>>> ACTG content number of A's = 44,010,137 bp (27.27%) number of C's = 28,799,543 bp (17.84%) number of T's = 52,102,672 bp (32.28%) number of G's = 36,404,397 bp (22.56%) number of N's = 78,841 bp (0.05%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,403,777 number of insertions = 12,322 mapped reads with insertion percentage = 0.49% number of deletions = 48,353 mapped reads with deletion percentage = 1.92% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0522X std coverageData = 0.4055X There is a 4.3% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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% 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 12206730 0.04897371950780415 0.6240288833237414 chr2 243199373 16193328 0.06658457955810601 0.5204126654185257 chr3 198022430 9297271 0.04695059544517255 0.2535208015339145 chr4 191154276 10709087 0.05602326677745885 0.2896212831711975 chr5 180915260 8013099 0.044292001680786904 0.24714693071532 chr6 171115067 9345749 0.05461675096091918 0.3339481655002599 chr7 159138663 10273789 0.0645587238595815 0.6225827642050977 chr8 146364022 8484818 0.05797065347111054 0.5672508214213584 chr9 141213431 6053043 0.042864499199088225 0.37415315581228165 chr10 135534747 8259650 0.0609411990860174 0.3800597941637122 chr11 135006516 8094061 0.05995311367045425 0.39621057662690784 chr12 133851895 7404093 0.055315563518917685 0.28155822942259695 chr13 115169878 4878543 0.04235953953168206 0.2390736742753161 chr14 107349540 4998724 0.0465649317174531 0.26314345703573583 chr15 102531392 4850248 0.04730500489059975 0.2578516846488646 chr16 90354753 3769059 0.04171400922317833 0.26529735582018044 chr17 81195210 4026793 0.04959397235378787 0.28979224367983797 chr18 78077248 4645123 0.05949393861832835 0.6427995238472336 chr19 59128983 2520127 0.04262084128861137 0.4453722320510603 chr20 63025520 3139076 0.04980642761852659 0.27071312236012707 chr21 48129895 2304202 0.04787465254183496 0.2693202832658626 chr22 51304566 1530732 0.02983617481531761 0.19787443167664356 chrMT 16571 4547 0.2743950274576067 0.6274971043983495 chrX 155270560 10050947 0.06473182681894107 0.3353974597364003 chrY 59373566 422690 0.007119161412673108 0.1488798294822465