BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525174.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,120,643 number of mapped reads = 1,030,531 (91.96%) number of supplementary alignments = 3,869 (0.35%) number of secondary alignments = 0 number of mapped bases = 63,845,798 bp number of sequenced bases = 63,824,649 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,162 duplication rate = 1.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7489 >>>>>>> ACTG content number of A's = 17,401,900 bp (27.27%) number of C's = 13,292,197 bp (20.83%) number of T's = 18,842,280 bp (29.52%) number of G's = 14,286,692 bp (22.38%) number of N's = 1,580 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 306,806 number of insertions = 5,645 mapped reads with insertion percentage = 0.55% number of deletions = 13,151 mapped reads with deletion percentage = 1.27% homopolymer indels = 41.52% >>>>>>> Coverage mean coverageData = 0.0206X std coverageData = 0.2212X There is a 1.92% of reference with a coverageData >= 1X There is a 0.1% 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 7071616 0.02837150804932197 0.44491691687937146 chr2 243199373 5418896 0.02228170218185554 0.2221870001321205 chr3 198022430 5184007 0.02617888791688901 0.17105109613048874 chr4 191154276 3641304 0.01904903241609934 0.14856545910816688 chr5 180915260 2948080 0.016295363917891725 0.1343388675493126 chr6 171115067 3246776 0.018974226273131167 0.15954407586715486 chr7 159138663 3795060 0.023847504613005326 0.32178159837646 chr8 146364022 2882492 0.019693992831107086 0.1743136347312155 chr9 141213431 2013184 0.014256320986918022 0.15744409042135768 chr10 135534747 3567965 0.026325094331714066 0.24559408288742718 chr11 135006516 2985246 0.022111866067264487 0.18247947898569333 chr12 133851895 2931408 0.021900384749875972 0.15679203905369576 chr13 115169878 2039900 0.017712096560526008 0.13954090232628524 chr14 107349540 2462679 0.022940750374896807 0.16354073583627277 chr15 102531392 1836370 0.017910319602410157 0.13980098658576487 chr16 90354753 1812098 0.020055369970409857 0.16342580190126177 chr17 81195210 1301328 0.016027152340636844 0.13754474025068542 chr18 78077248 1420828 0.01819772131312825 0.3093073167661627 chr19 59128983 1173318 0.019843365139562776 0.3116097578612494 chr20 63025520 1233514 0.019571659226294363 0.1477835599249202 chr21 48129895 833198 0.01731144437360605 0.1466129603204142 chr22 51304566 537568 0.010477975780947061 0.10695369473568513 chrMT 16571 35711 2.155029871462193 1.8125606663397804 chrX 155270560 3292387 0.0212041935058391 0.16225108972232574 chrY 59373566 180865 0.0030462209394665632 0.1010021728306913