BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524629.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 = 727,545 number of mapped reads = 669,984 (92.09%) number of supplementary alignments = 1,316 (0.18%) number of secondary alignments = 0 number of mapped bases = 38,711,591 bp number of sequenced bases = 38,699,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,498 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0919 >>>>>>> ACTG content number of A's = 9,778,883 bp (25.27%) number of C's = 7,088,669 bp (18.32%) number of T's = 12,546,165 bp (32.42%) number of G's = 9,285,609 bp (23.99%) number of N's = 288 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 184,304 number of insertions = 2,512 mapped reads with insertion percentage = 0.37% number of deletions = 7,061 mapped reads with deletion percentage = 1.05% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.0125X std coverageData = 0.136X There is a 1.17% of reference with a coverageData >= 1X There is a 0.06% 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 3934942 0.015787090055033405 0.18006523522895637 chr2 243199373 3434698 0.014122972266051031 0.15693813866460024 chr3 198022430 2481724 0.012532539874397057 0.11842764613276129 chr4 191154276 1774514 0.009283150956037206 0.10935279133499393 chr5 180915260 2423548 0.01339603967072761 0.12190391664337477 chr6 171115067 2530929 0.014790801560449379 0.13236145853762848 chr7 159138663 2336803 0.014684068320971126 0.1668415312766214 chr8 146364022 3408729 0.023289391432547542 0.18712714635732763 chr9 141213431 1447325 0.010249202145651429 0.12400416690098609 chr10 135534747 1673741 0.012349165339866684 0.13926442072792133 chr11 135006516 1881482 0.013936231048285107 0.14067597995516465 chr12 133851895 1211275 0.009049367586465623 0.10385237030478471 chr13 115169878 923707 0.008020387066833569 0.09536447703166896 chr14 107349540 709769 0.006611756324246942 0.08750017809780422 chr15 102531392 983235 0.00958959964183457 0.10827317744205912 chr16 90354753 1153434 0.0127656151082611 0.12179857821781434 chr17 81195210 859903 0.010590563162531385 0.10997215019398932 chr18 78077248 1066225 0.013656026913243663 0.18554492556387192 chr19 59128983 795374 0.013451508205375357 0.15363143984087813 chr20 63025520 736682 0.011688630256442152 0.11552737579939736 chr21 48129895 354261 0.007360518862548942 0.09304331773923745 chr22 51304566 688995 0.013429506449776809 0.12191779844649249 chrMT 16571 827 0.04990646309818357 0.23481938961168 chrX 155270560 1802814 0.011610790867244892 0.12068247001894512 chrY 59373566 96655 0.0016279130008798866 0.05552311010927607