BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008712.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 = 1,254,598 number of mapped reads = 1,047,891 (83.52%) number of supplementary alignments = 5,679 (0.45%) number of secondary alignments = 0 number of mapped bases = 69,809,116 bp number of sequenced bases = 69,776,978 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,205 duplication rate = 1.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0148 >>>>>>> ACTG content number of A's = 21,018,300 bp (30.12%) number of C's = 12,280,174 bp (17.6%) number of T's = 20,442,690 bp (29.3%) number of G's = 16,032,115 bp (22.98%) number of N's = 3,699 bp (0.01%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 570,945 number of insertions = 5,224 mapped reads with insertion percentage = 0.49% number of deletions = 19,985 mapped reads with deletion percentage = 1.88% homopolymer indels = 45.73% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.1897X There is a 2.13% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 7537319 0.03023992064597504 0.283668346515973 chr2 243199373 6989622 0.02874029613554966 0.21403381986701409 chr3 198022430 5772504 0.02915075832571088 0.18199889962853552 chr4 191154276 2730716 0.014285403691414154 0.12682373596080931 chr5 180915260 3277205 0.018114585801109313 0.13845456327726915 chr6 171115067 3758966 0.0219674752545315 0.16459209122103238 chr7 159138663 4219369 0.026513789424006912 0.2297325281780975 chr8 146364022 4768011 0.032576386839109954 0.21657636042064693 chr9 141213431 1864433 0.013202943847458815 0.14238012532790353 chr10 135534747 3134759 0.023128821718315526 0.28279822699073304 chr11 135006516 2578906 0.01910208541341812 0.16660753120069552 chr12 133851895 3060573 0.022865369220211637 0.1560129923032151 chr13 115169878 2294911 0.019926312677000492 0.14551912066828762 chr14 107349540 3155924 0.029398579630616022 0.18057082403538818 chr15 102531392 1886491 0.01839915525578742 0.14144051160047044 chr16 90354753 1578142 0.01746606512221886 0.14860769886904335 chr17 81195210 1869862 0.02302921563969106 0.16693757392355205 chr18 78077248 814930 0.010437483657210868 0.21767739302923084 chr19 59128983 1098216 0.018573226601918725 0.18077328076367383 chr20 63025520 1906482 0.03024936565378596 0.18163450821149368 chr21 48129895 936896 0.01946598886201601 0.14838909133961692 chr22 51304566 737864 0.014382033755046287 0.12394216218072707 chrMT 16571 12378 0.7469675939894997 1.008263084873914 chrX 155270560 3656409 0.023548630210388884 0.16447936595821197 chrY 59373566 168228 0.0028333821148623616 0.07665485842243329