BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716685.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 = 1,505,268 number of mapped reads = 1,319,565 (87.66%) number of supplementary alignments = 4,003 (0.27%) number of secondary alignments = 0 number of mapped bases = 74,866,845 bp number of sequenced bases = 74,844,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,181 duplication rate = 1.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8377 >>>>>>> ACTG content number of A's = 19,163,349 bp (25.6%) number of C's = 14,487,964 bp (19.36%) number of T's = 22,518,284 bp (30.09%) number of G's = 18,674,849 bp (24.95%) number of N's = 477 bp (0%) GC percentage = 44.31% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 392,153 number of insertions = 5,738 mapped reads with insertion percentage = 0.43% number of deletions = 13,768 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.69% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2174X There is a 2.21% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 6280595 0.025197911141814164 0.2443282804500486 chr2 243199373 5873356 0.024150374762684935 0.34375763183994207 chr3 198022430 4316527 0.021798172055559565 0.16470685150782227 chr4 191154276 4528918 0.023692475495552087 0.1779449460428337 chr5 180915260 4183308 0.023123024558569575 0.16239893117298534 chr6 171115067 3970973 0.023206448558968803 0.19325475974752804 chr7 159138663 4276501 0.02687279709017035 0.29938626158539816 chr8 146364022 3848832 0.026296298416833612 0.20400467186652385 chr9 141213431 2491866 0.017646097700154316 0.16330998402152863 chr10 135534747 3334545 0.02460287914212877 0.27699412976100196 chr11 135006516 2656469 0.019676598424330866 0.17582156954490694 chr12 133851895 3761312 0.02810055098584895 0.18146318892001895 chr13 115169878 2237371 0.019426702874513768 0.14872349502643437 chr14 107349540 2496423 0.023255088005034768 0.16777238727138166 chr15 102531392 2763951 0.026957119630249438 0.17928437685836998 chr16 90354753 2633165 0.029142517826372675 0.19519390420268926 chr17 81195210 3427245 0.04220994070955664 0.230199695406979 chr18 78077248 1380815 0.01768524167245239 0.24471752267888308 chr19 59128983 2054466 0.03474549866687205 0.2624715910664299 chr20 63025520 2396128 0.03801837731763261 0.21857274772178265 chr21 48129895 944604 0.019626138806245058 0.16090230811675257 chr22 51304566 728523 0.014199964190321773 0.12942960299491732 chrMT 16571 63796 3.8498581859875687 3.1840969781349213 chrX 155270560 3987136 0.025678634765019203 0.18365197860175714 chrY 59373566 230020 0.0038741146186166415 0.11505926618273496