BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716432.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 = 3,907,819 number of mapped reads = 3,512,738 (89.89%) number of supplementary alignments = 70,430 (1.8%) number of secondary alignments = 0 number of mapped bases = 267,944,882 bp number of sequenced bases = 267,849,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 197,194 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7404 >>>>>>> ACTG content number of A's = 67,748,134 bp (25.29%) number of C's = 55,911,723 bp (20.87%) number of T's = 81,457,191 bp (30.41%) number of G's = 62,699,098 bp (23.41%) number of N's = 33,837 bp (0.01%) GC percentage = 44.28% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,939,466 number of insertions = 22,296 mapped reads with insertion percentage = 0.63% number of deletions = 55,371 mapped reads with deletion percentage = 1.56% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.0866X std coverageData = 0.6046X There is a 6.59% of reference with a coverageData >= 1X There is a 1.36% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 21270881 0.08533933000712564 0.695982375796467 chr2 243199373 22944892 0.09434601626213897 0.9188743728127283 chr3 198022430 17755071 0.08966191860184727 0.3752936308945598 chr4 191154276 17004295 0.08895587038816752 0.42630434492666847 chr5 180915260 16315310 0.09018205539985959 0.38243027382350714 chr6 171115067 15360937 0.08976963437123862 0.45050619560054894 chr7 159138663 14489231 0.09104783669069785 0.7723277270167459 chr8 146364022 13640993 0.09319908549657101 0.7922681480872802 chr9 141213431 11252774 0.0796862870642949 0.676257517964645 chr10 135534747 12690662 0.09363401106286051 0.554738528502446 chr11 135006516 12290473 0.09103614672939193 0.663378465063472 chr12 133851895 11908823 0.08897014868560509 0.3874546329890465 chr13 115169878 8411895 0.07303901980342464 0.33871574819973077 chr14 107349540 8241700 0.0767744323822906 0.43871910476125814 chr15 102531392 7690007 0.07500148832466841 0.34813869971724826 chr16 90354753 8025427 0.08882130417643884 0.4336165570273534 chr17 81195210 7444937 0.09169182517047496 0.42636572905287723 chr18 78077248 7340088 0.09401058807810439 1.2947409590616128 chr19 59128983 5634313 0.09528851527853946 0.6566727766321079 chr20 63025520 5812968 0.09223197206464936 0.4111568595369001 chr21 48129895 3556575 0.07389534093103672 0.3949593172786935 chr22 51304566 3229418 0.0629460153702499 0.31903829487691066 chrMT 16571 35096 2.1179168426769657 2.328765597034905 chrX 155270560 14935533 0.09619037246983587 0.5424232248323264 chrY 59373566 662583 0.011159562152625294 0.2926454929612008