BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524384.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 = 1,465,463 number of mapped reads = 1,359,893 (92.8%) number of supplementary alignments = 5,517 (0.38%) number of secondary alignments = 0 number of mapped bases = 79,775,241 bp number of sequenced bases = 79,753,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,819 duplication rate = 2.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8337 >>>>>>> ACTG content number of A's = 20,510,793 bp (25.72%) number of C's = 15,614,457 bp (19.58%) number of T's = 24,796,278 bp (31.09%) number of G's = 18,820,764 bp (23.6%) number of N's = 10,916 bp (0.01%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 380,833 number of insertions = 5,951 mapped reads with insertion percentage = 0.44% number of deletions = 14,042 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.83% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.2599X There is a 2.33% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6563413 0.02633258434288916 0.5326535782062525 chr2 243199373 6558886 0.026969173148320577 0.2765505268749382 chr3 198022430 5389578 0.027217007689482448 0.1780961894936029 chr4 191154276 5356192 0.028020257312998845 0.19596235461363318 chr5 180915260 4891600 0.02703807296299936 0.17685837349407524 chr6 171115067 3062737 0.017898698540672633 0.15440978154404084 chr7 159138663 4637197 0.02913934874518834 0.34341121373618083 chr8 146364022 4179626 0.02855637569183498 0.2346311369680008 chr9 141213431 2978944 0.021095330514276648 0.19928657604212557 chr10 135534747 3957371 0.029198202583430505 0.24043155690154513 chr11 135006516 3364810 0.024923315553154485 0.21555395107417857 chr12 133851895 3734290 0.02789867113947098 0.18764503085939618 chr13 115169878 2537945 0.022036534587628893 0.1601888629949455 chr14 107349540 2251950 0.02097773311371432 0.16106753942768132 chr15 102531392 2423818 0.023639764882934584 0.16707820040885507 chr16 90354753 2429279 0.02688601229422873 0.18549612120419823 chr17 81195210 2192722 0.02700555857913293 0.19149215209834403 chr18 78077248 2174287 0.02784789494629729 0.3482908967019542 chr19 59128983 2231492 0.03773939423243589 0.37990165196568076 chr20 63025520 2232294 0.035418890633508456 0.2096264171345005 chr21 48129895 1110163 0.023065975938655173 0.18037468929045083 chr22 51304566 562695 0.010967737257537663 0.11219876509137808 chrMT 16571 22185 1.3387846237402692 1.4668179919377442 chrX 155270560 4687767 0.03019095828597514 0.203763674101674 chrY 59373566 244000 0.004109572936885752 0.11883409632870877