BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013167.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 = 2,195,999 number of mapped reads = 1,501,780 (68.39%) number of supplementary alignments = 11,369 (0.52%) number of secondary alignments = 0 number of mapped bases = 93,512,179 bp number of sequenced bases = 93,446,772 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 425,406 duplication rate = 16.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1705 >>>>>>> ACTG content number of A's = 24,941,788 bp (26.69%) number of C's = 16,860,894 bp (18.04%) number of T's = 29,903,256 bp (32%) number of G's = 21,603,217 bp (23.12%) number of N's = 137,617 bp (0.15%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 943,631 number of insertions = 6,494 mapped reads with insertion percentage = 0.43% number of deletions = 37,835 mapped reads with deletion percentage = 2.48% homopolymer indels = 43.68% >>>>>>> Coverage mean coverageData = 0.0302X std coverageData = 0.4906X There is a 1.01% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 6363601 0.025530933381305396 0.5087734517712911 chr2 243199373 12665415 0.05207832094205276 0.6868659293483601 chr3 198022430 6018925 0.03039516786052974 0.46816079290210666 chr4 191154276 6210671 0.032490358729929746 0.46539157923634894 chr5 180915260 4565722 0.025236798708964628 0.41935966657559687 chr6 171115067 4938313 0.02885960357891804 0.4687185087171692 chr7 159138663 5223944 0.03282636602269305 0.6157140440870309 chr8 146364022 6433664 0.04395659474293485 0.5719826537737364 chr9 141213431 3154147 0.02233602694633204 0.4161426118712899 chr10 135534747 4950521 0.03652584381184553 0.5310230876572761 chr11 135006516 3901718 0.028900219897534427 0.4607335001358802 chr12 133851895 3940642 0.02944031535750764 0.4491699343953609 chr13 115169878 2115442 0.01836801459492733 0.3593657986231283 chr14 107349540 2328709 0.021692771110151006 0.3835068304711461 chr15 102531392 2740152 0.026725005352507065 0.44510868255902464 chr16 90354753 2980818 0.03299016267578087 0.49167411736523164 chr17 81195210 2553874 0.031453505693254565 0.4646852103417244 chr18 78077248 2109020 0.027011966405373303 0.5275197436700118 chr19 59128983 1654162 0.0279754853892887 0.4788324104292924 chr20 63025520 2220525 0.0352321567517412 0.4967263920240952 chr21 48129895 1380548 0.0286837941366795 0.43933399789223343 chr22 51304566 874535 0.017045948697821556 0.33861034935494766 chrMT 16571 66986 4.042363164564601 5.631969618782977 chrX 155270560 3873704 0.024948090610351376 0.41129659846113215 chrY 59373566 246421 0.004150348658525917 0.14624349297093203