BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236081.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 = 2,890,567 number of mapped reads = 2,558,442 (88.51%) number of supplementary alignments = 19,090 (0.66%) number of secondary alignments = 0 number of mapped bases = 164,550,424 bp number of sequenced bases = 164,471,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,763 duplication rate = 4.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2127 >>>>>>> ACTG content number of A's = 46,319,473 bp (28.16%) number of C's = 30,682,584 bp (18.66%) number of T's = 51,194,330 bp (31.13%) number of G's = 36,273,886 bp (22.05%) number of N's = 1,448 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,222,706 number of insertions = 12,014 mapped reads with insertion percentage = 0.47% number of deletions = 46,351 mapped reads with deletion percentage = 1.79% homopolymer indels = 46.69% >>>>>>> Coverage mean coverageData = 0.0532X std coverageData = 0.4825X There is a 4.19% of reference with a coverageData >= 1X There is a 0.8% 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 15234948 0.06112300919803927 0.5907754459545268 chr2 243199373 9867969 0.040575635036690656 0.529934445363444 chr3 198022430 15825701 0.07991872940858265 0.3456426702403357 chr4 191154276 7800146 0.040805500997529345 0.29609988196468706 chr5 180915260 6471063 0.03576847525189417 0.23166855984552392 chr6 171115067 19318324 0.11289668606447145 0.5989057334275539 chr7 159138663 10245878 0.06438333593389559 0.6041646440800059 chr8 146364022 10442177 0.07134387848401706 1.2653713552167318 chr9 141213431 4645794 0.032899094421124854 0.33036136385244597 chr10 135534747 6328781 0.04669489662307777 0.3335667080520101 chr11 135006516 5596238 0.04145161408357505 0.3518030524101646 chr12 133851895 4770194 0.03563785182122375 0.23415580871215477 chr13 115169878 8160494 0.07085614868846175 0.3322472157010902 chr14 107349540 5369007 0.05001425250634516 0.2810778400561778 chr15 102531392 4198154 0.040945060026104006 0.2678698669000854 chr16 90354753 4249702 0.04703351908891832 0.2763550972246938 chr17 81195210 4233322 0.05213758299288837 0.30338662421112333 chr18 78077248 4512055 0.057789626499130706 0.5449279461720647 chr19 59128983 3793086 0.0641493529492973 0.5108271999501143 chr20 63025520 2634678 0.041803352038983575 0.25235887320792116 chr21 48129895 2630566 0.05465555243783515 0.2945121139227899 chr22 51304566 1408098 0.027445861251413763 0.19539052905608098 chrMT 16571 113107 6.825598937903567 5.927956340200513 chrX 155270560 6382458 0.0411053969277885 0.27319031548946854 chrY 59373566 318484 0.005364070603406237 0.1241800335251095