BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716670.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 = 1,691,016 number of mapped reads = 1,554,054 (91.9%) number of supplementary alignments = 8,749 (0.52%) number of secondary alignments = 0 number of mapped bases = 91,112,225 bp number of sequenced bases = 91,086,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,242 duplication rate = 3.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0635 >>>>>>> ACTG content number of A's = 22,009,572 bp (24.16%) number of C's = 17,414,233 bp (19.12%) number of T's = 28,769,062 bp (31.58%) number of G's = 22,893,038 bp (25.13%) number of N's = 687 bp (0%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 455,828 number of insertions = 6,224 mapped reads with insertion percentage = 0.4% number of deletions = 16,225 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.0294X std coverageData = 0.2656X There is a 2.6% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 10828916 0.04344589376168495 0.42750678331338715 chr2 243199373 9312138 0.038290139835187816 0.370022999381459 chr3 198022430 5729822 0.02893521708626644 0.18710550257506778 chr4 191154276 3804562 0.01990309649154801 0.1786709145974475 chr5 180915260 6509108 0.03597876707581218 0.20966996540300573 chr6 171115067 3381690 0.01976266648687342 0.17429665295790162 chr7 159138663 6061071 0.03808672817616923 0.40215918057329575 chr8 146364022 4082321 0.027891560673291693 0.24003556915935548 chr9 141213431 2495764 0.017673701306782922 0.1938362204183718 chr10 135534747 4101473 0.030261413333364618 0.2424396729432367 chr11 135006516 3853596 0.028543777842545023 0.2472173985307894 chr12 133851895 3631851 0.027133355116115466 0.18285837417418754 chr13 115169878 2618903 0.022739478807123507 0.16723062998540122 chr14 107349540 1937523 0.018048731275420463 0.15617642205928609 chr15 102531392 3971626 0.0387357074016902 0.2183910870610761 chr16 90354753 2710067 0.029993629665503042 0.20113046827201275 chr17 81195210 3453152 0.042529011255713234 0.24536569226682908 chr18 78077248 2898096 0.03711831646525247 0.4459261154109222 chr19 59128983 1428685 0.024162177793587283 0.3181056240980477 chr20 63025520 2380874 0.03777634837443626 0.21848878048394899 chr21 48129895 1179468 0.02450593337051743 0.18650174765656818 chr22 51304566 1090832 0.021261889243932013 0.16081775447978858 chrMT 16571 37557 2.2664293042061434 2.066744476292768 chrX 155270560 3397052 0.021878274928614928 0.18391382762858494 chrY 59373566 216078 0.0036392963158049154 0.10654274968594667