BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524738.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 = 1,702,349 number of mapped reads = 1,543,196 (90.65%) number of supplementary alignments = 7,023 (0.41%) number of secondary alignments = 0 number of mapped bases = 88,422,784 bp number of sequenced bases = 88,393,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,402 duplication rate = 3.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.389 >>>>>>> ACTG content number of A's = 22,711,883 bp (25.69%) number of C's = 16,421,791 bp (18.58%) number of T's = 27,155,991 bp (30.72%) number of G's = 22,093,184 bp (24.99%) number of N's = 10,630 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 457,301 number of insertions = 6,955 mapped reads with insertion percentage = 0.45% number of deletions = 17,798 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.32% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2536X There is a 2.54% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 7074457 0.028382906215507483 0.34253663321776084 chr2 243199373 7452249 0.030642550217430044 0.4141019804608075 chr3 198022430 5767817 0.02912708928983449 0.19268883827586508 chr4 191154276 5669693 0.029660299097886776 0.21739112312699735 chr5 180915260 5250682 0.02902288065694403 0.18740220056161486 chr6 171115067 5026696 0.02937611566373638 0.20961753014532797 chr7 159138663 4892701 0.030744891956268353 0.3010523397522903 chr8 146364022 4413048 0.03015118018552401 0.23751178102305118 chr9 141213431 3765963 0.026668589335528573 0.21831565313455856 chr10 135534747 4303056 0.03174872934982496 0.3057258823902813 chr11 135006516 4000424 0.02963134016435177 0.22823824326842065 chr12 133851895 3991790 0.02982243919669572 0.1923630927407705 chr13 115169878 2679141 0.023262514873897844 0.1690133185077017 chr14 107349540 2666134 0.02483600768107623 0.17798186516235137 chr15 102531392 2540156 0.024774422256941563 0.17388678632039223 chr16 90354753 2671880 0.02957099556234745 0.20943938225743908 chr17 81195210 2538238 0.03126093275699392 0.20350263631821502 chr18 78077248 2312774 0.029621612687988182 0.314973605375328 chr19 59128983 1958193 0.03311731236777741 0.2913933526417872 chr20 63025520 1914121 0.030370570524447874 0.20053801438400354 chr21 48129895 1167233 0.024251725460859616 0.195892448140868 chr22 51304566 1139420 0.022208939453849 0.1656582474365576 chrMT 16571 33613 2.02842314887454 1.8500278288483996 chrX 155270560 4899180 0.0315525364241618 0.2102913917067519 chrY 59373566 294125 0.004953803852711154 0.13870203448790985