BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779216.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 7,078,610 number of mapped reads = 6,871,277 (97.07%) number of supplementary alignments = 16,728 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,472,884 number of mapped paired reads (second in pair) = 3,398,393 number of mapped paired reads (both in pair) = 6,787,040 number of mapped paired reads (singletons) = 84,237 number of mapped bases = 546,489,614 bp number of sequenced bases = 546,381,037 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,441 duplication rate = 0.71% >>>>>>> Insert size mean insert size = 56,604.9955 std insert size = 2,244,462.175 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.0918 >>>>>>> ACTG content number of A's = 167,436,117 bp (30.64%) number of C's = 104,952,257 bp (19.21%) number of T's = 166,804,087 bp (30.53%) number of G's = 107,088,236 bp (19.6%) number of N's = 100,340 bp (0.02%) GC percentage = 38.81% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 2,438,601 number of insertions = 41,794 mapped reads with insertion percentage = 0.6% number of deletions = 52,893 mapped reads with deletion percentage = 0.76% homopolymer indels = 47.18% >>>>>>> Coverage mean coverageData = 0.1765X std coverageData = 0.5597X There is a 13.63% of reference with a coverageData >= 1X There is a 2.85% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 40862167 0.16394008101588642 0.588129337289301 chr2 243199373 43949417 0.18071352922443595 0.499954259601124 chr3 198022430 38745575 0.19566255701437457 0.5155333482996598 chr4 191154276 36806004 0.1925460668219632 0.5105526936033201 chr5 180915260 36821485 0.20352890629568782 0.526050520511975 chr6 171115067 33313784 0.19468644453150347 0.5205218457583577 chr7 159138663 51652165 0.3245733250881968 1.1706594899122198 chr8 146364022 40105876 0.2740145798945044 0.626245599079899 chr9 141213431 21068272 0.14919453376924183 0.46895297808180175 chr10 135534747 13237873 0.09767143328935421 0.5126296872770759 chr11 135006516 22358896 0.16561345824226736 0.47850918413053056 chr12 133851895 25143913 0.18784876373995302 0.507452634947353 chr13 115169878 17369625 0.1508174298838799 0.45422121148704486 chr14 107349540 14955042 0.13931165424649233 0.4415514960199161 chr15 102531392 12532608 0.12223191117896849 0.41427878264289164 chr16 90354753 9212597 0.10196029200588927 0.37071129175736 chr17 81195210 8816290 0.10858140523314122 0.39125772983970375 chr18 78077248 14333906 0.18358620939098674 0.5065562566361221 chr19 59128983 6367555 0.10768923592005633 0.42370495147833775 chr20 63025520 11062827 0.17552932526379791 0.5075886283489642 chr21 48129895 6631863 0.1377909301485075 0.4484967865651926 chr22 51304566 2800765 0.054590950053061554 0.27048753170466383 chrMT 16571 698 0.04212177901152616 0.22415249813573548 chrX 155270560 37967192 0.24452279942830116 0.6068357299574728 chrY 59373566 373219 0.006285945499719521 0.09968219599471081