BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008730.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 = 3,300,963 number of mapped reads = 2,925,667 (88.63%) number of supplementary alignments = 19,145 (0.58%) number of secondary alignments = 0 number of mapped bases = 186,423,128 bp number of sequenced bases = 186,315,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,363 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3322 >>>>>>> ACTG content number of A's = 48,821,429 bp (26.2%) number of C's = 34,267,648 bp (18.39%) number of T's = 57,656,778 bp (30.95%) number of G's = 45,436,690 bp (24.39%) number of N's = 133,152 bp (0.07%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,567,401 number of insertions = 13,698 mapped reads with insertion percentage = 0.46% number of deletions = 63,596 mapped reads with deletion percentage = 2.15% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.4972X There is a 4.8% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 14932693 0.059910354245416304 0.9071626077298601 chr2 243199373 17691992 0.07274686518209074 0.8122417593902812 chr3 198022430 13314731 0.06723849919425795 0.31359260126509003 chr4 191154276 8933931 0.04673675727766613 0.2756300615211265 chr5 180915260 7674813 0.04242214283084799 0.25172779692285613 chr6 171115067 8050116 0.047045044841083454 0.321019123617717 chr7 159138663 10400275 0.06535354013876565 0.5508431111219174 chr8 146364022 14918773 0.1019292364075647 0.5896066837795111 chr9 141213431 5886129 0.041682501149625066 0.41683064172553697 chr10 135534747 11026363 0.08135451051529981 0.43477325277572115 chr11 135006516 8442338 0.06253281878631695 0.4721979507498682 chr12 133851895 7669096 0.0572953860683108 0.29555088617211045 chr13 115169878 4699293 0.04080314298848176 0.24189897881048264 chr14 107349540 6168086 0.05745796395587722 0.3015228949086827 chr15 102531392 4743049 0.04625948119381818 0.28142870248231927 chr16 90354753 6119735 0.06773008388391034 0.3750025733686128 chr17 81195210 6786129 0.08357794751685475 0.42422332965994997 chr18 78077248 2649948 0.03394007944542308 0.6166819377692049 chr19 59128983 5391383 0.09118003940639398 0.6339701564826024 chr20 63025520 5100930 0.0809343580187835 0.35539542584655226 chr21 48129895 2305340 0.047898296890113726 0.27874311958186954 chr22 51304566 3117905 0.06077246613878383 0.2973662930065104 chrMT 16571 136686 8.248506426890351 6.549650029017515 chrX 155270560 9767697 0.06290759175467649 0.34968419653538807 chrY 59373566 495697 0.008348782688915805 0.18374183987103765