BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714111.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 586,750 number of mapped reads = 462,104 (78.76%) number of supplementary alignments = 16,550 (2.82%) number of secondary alignments = 0 number of mapped bases = 59,663,764 bp number of sequenced bases = 58,560,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 387,313 duplication rate = 43.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5412 >>>>>>> ACTG content number of A's = 16,448,141 bp (28.09%) number of C's = 12,458,855 bp (21.28%) number of T's = 15,591,581 bp (26.62%) number of G's = 14,061,585 bp (24.01%) number of N's = 468 bp (0%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.0419 number of mismatches = 2,232,952 number of insertions = 67,830 mapped reads with insertion percentage = 14.27% number of deletions = 194,755 mapped reads with deletion percentage = 40.26% homopolymer indels = 28.82% >>>>>>> Coverage mean coverageData = 0.0193X std coverageData = 2.3369X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4988036 0.020012130681913126 2.1227699074666413 chr2 243199373 5944139 0.024441424032783175 4.539017264267355 chr3 198022430 3145931 0.01588674070912068 1.461878303855884 chr4 191154276 3219430 0.016842050658599967 1.8711590237181748 chr5 180915260 3074908 0.01699639930871503 1.597351948697852 chr6 171115067 2597587 0.01518035229475146 1.4819736302676012 chr7 159138663 2504457 0.01573757723476664 1.5955359705360637 chr8 146364022 2816185 0.019240964832190795 2.1726560527615186 chr9 141213431 2191786 0.015521087367390713 1.870075233735388 chr10 135534747 3262871 0.02407405534169035 2.1632019019372786 chr11 135006516 2677902 0.019835353724704664 1.8885402423496473 chr12 133851895 2414557 0.018039019918246208 1.706027874623139 chr13 115169878 1738572 0.015095717996679652 1.5502263228372088 chr14 107349540 2011270 0.018735711396620797 1.9450170553910504 chr15 102531392 1729891 0.016871818145217418 1.7262275989985465 chr16 90354753 1802693 0.019951280260818154 2.111601668105349 chr17 81195210 2281755 0.02810208878085296 2.9935310043064773 chr18 78077248 1676231 0.02146887912852666 2.1102471606887185 chr19 59128983 1027187 0.017371971373158913 1.8458869950861838 chr20 63025520 1590977 0.0252433776032312 2.292691517645559 chr21 48129895 496480 0.010315418307062585 1.0358659437832958 chr22 51304566 660342 0.012871018146805881 1.5749934853079346 chrMT 16571 597442 36.053466900006036 332.716164974352 chrX 155270560 4997064 0.03218294569170099 2.10166719479625 chrY 59373566 216071 0.0036391784182206607 0.6819619028766473