BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524839.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 = 935,738 number of mapped reads = 865,860 (92.53%) number of supplementary alignments = 5,927 (0.63%) number of secondary alignments = 0 number of mapped bases = 50,728,860 bp number of sequenced bases = 50,714,041 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,116 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6462 >>>>>>> ACTG content number of A's = 13,943,039 bp (27.49%) number of C's = 8,705,782 bp (17.17%) number of T's = 16,168,203 bp (31.88%) number of G's = 11,890,688 bp (23.45%) number of N's = 6,329 bp (0.01%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 243,028 number of insertions = 4,636 mapped reads with insertion percentage = 0.53% number of deletions = 9,491 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 0.1817X There is a 1.53% of reference with a coverageData >= 1X There is a 0.07% 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 4190882 0.016813928018257575 0.3151531724663358 chr2 243199373 3313831 0.013625984965018803 0.1739905349181204 chr3 198022430 3645627 0.018410172019402045 0.14128550300254866 chr4 191154276 2803658 0.014666990760907698 0.13171696586609366 chr5 180915260 3079934 0.017024180270917996 0.13609593210401955 chr6 171115067 3318566 0.0193937685218567 0.15485945650544877 chr7 159138663 2340049 0.014704465626935675 0.2384618223941751 chr8 146364022 5535872 0.03782262829590731 0.2592727049622348 chr9 141213431 2096803 0.014848467211309384 0.16218695527199747 chr10 135534747 2531530 0.018678088505230322 0.17966953864834795 chr11 135006516 2482754 0.01838988275202954 0.17111532908789995 chr12 133851895 2004473 0.014975305355221158 0.12860126743215186 chr13 115169878 1371012 0.011904258507593453 0.1144320966153152 chr14 107349540 1064202 0.009913428599694046 0.10848799819654077 chr15 102531392 1519851 0.01482327480738777 0.12766128885270794 chr16 90354753 1423084 0.01574996281601257 0.13753822828252285 chr17 81195210 1310770 0.016143439988639725 0.1402357667998064 chr18 78077248 1237288 0.015846972475259374 0.26891894034541153 chr19 59128983 687862 0.011633245915966456 0.21673489986208339 chr20 63025520 1029766 0.016338873522979264 0.13448813088925096 chr21 48129895 724424 0.015051435287776962 0.13288305075117882 chr22 51304566 282538 0.005507073191107396 0.07710744632925204 chrMT 16571 800 0.048277110614929696 0.21435118662046995 chrX 155270560 2607393 0.016792578065024044 0.14769803384961336 chrY 59373566 125891 0.002120320682776574 0.061978446216438006