BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008782.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 = 1,197,972 number of mapped reads = 1,058,121 (88.33%) number of supplementary alignments = 6,079 (0.51%) number of secondary alignments = 0 number of mapped bases = 69,643,286 bp number of sequenced bases = 69,612,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,776 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0454 >>>>>>> ACTG content number of A's = 18,591,007 bp (26.71%) number of C's = 13,457,918 bp (19.33%) number of T's = 21,465,102 bp (30.83%) number of G's = 15,984,998 bp (22.96%) number of N's = 113,854 bp (0.16%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 562,777 number of insertions = 4,834 mapped reads with insertion percentage = 0.45% number of deletions = 16,997 mapped reads with deletion percentage = 1.59% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.0225X std coverageData = 0.2216X There is a 1.86% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.06% 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 4887788 0.01960993308819078 0.26148880620201137 chr2 243199373 6838611 0.028119361146543745 0.3115376150121896 chr3 198022430 5093760 0.025723146615259696 0.19045193847597433 chr4 191154276 3890306 0.020351655643842358 0.17259731059555042 chr5 180915260 2563263 0.014168307305862424 0.13815136375205597 chr6 171115067 4306326 0.025166258445260114 0.20067792366580745 chr7 159138663 3518176 0.022107613157463814 0.31670171543527115 chr8 146364022 3695309 0.02524738627365679 0.25023056455607084 chr9 141213431 1336428 0.009463887326694866 0.13574827355885247 chr10 135534747 4691734 0.03461646628521024 0.2738318571178206 chr11 135006516 2848602 0.02109973714157619 0.21943428651374214 chr12 133851895 2742768 0.020491065890400728 0.167946962473885 chr13 115169878 1528855 0.013274781796677773 0.13452337322592178 chr14 107349540 3015981 0.02809495969894235 0.19808821742846977 chr15 102531392 1584448 0.015453296488942626 0.1446111066442478 chr16 90354753 2642557 0.02924646365864118 0.2208677304331019 chr17 81195210 2447248 0.030140300148247662 0.22320034781044856 chr18 78077248 1282985 0.016432251812973735 0.25350829516329537 chr19 59128983 1775056 0.030020066470617293 0.25419573262687795 chr20 63025520 1900639 0.030156657176331113 0.208252964995097 chr21 48129895 1105412 0.022967263901157484 0.18598118389440557 chr22 51304566 1088260 0.021211757253730593 0.17093467440985427 chrMT 16571 108315 6.536419045320137 4.730754034065879 chrX 155270560 4554709 0.029334015411550007 0.20807099100968848 chrY 59373566 195750 0.0032969217311286307 0.08444037975347175