BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230345.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,487,774 number of mapped reads = 1,282,801 (86.22%) number of supplementary alignments = 10,180 (0.68%) number of secondary alignments = 0 number of mapped bases = 88,739,577 bp number of sequenced bases = 88,692,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,697 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5705 >>>>>>> ACTG content number of A's = 26,433,316 bp (29.8%) number of C's = 16,810,841 bp (18.95%) number of T's = 26,902,920 bp (30.33%) number of G's = 18,501,723 bp (20.86%) number of N's = 43,479 bp (0.05%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 852,387 number of insertions = 8,145 mapped reads with insertion percentage = 0.63% number of deletions = 28,349 mapped reads with deletion percentage = 2.18% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.3415X There is a 2.57% of reference with a coverageData >= 1X There is a 0.2% 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 7185444 0.028828188957651584 0.6841979440334328 chr2 243199373 7430716 0.030554009693108872 0.3082205244253289 chr3 198022430 5877497 0.02968096593906054 0.18444489251165094 chr4 191154276 6076436 0.03178812489656261 0.21062309890448846 chr5 180915260 5385933 0.02977047375660848 0.18645496381435325 chr6 171115067 5350241 0.03126691935316251 0.21939981533222339 chr7 159138663 4987114 0.03133816701727599 0.3757210131938799 chr8 146364022 4680917 0.0319813362330259 0.6503090954863435 chr9 141213431 3754605 0.026588157892714893 0.2855499250328881 chr10 135534747 4244302 0.03131523165790098 0.2948414881560908 chr11 135006516 3984286 0.02951180519316564 0.29625946635120787 chr12 133851895 3943486 0.029461562721992095 0.18825329556011294 chr13 115169878 2885923 0.025057966979872982 0.1698130871539657 chr14 107349540 2856680 0.026611012958229725 0.18737111976188173 chr15 102531392 2458496 0.023977983250242033 0.16636309181183173 chr16 90354753 2249198 0.024892968275836026 0.19929833634169253 chr17 81195210 2015843 0.024827117264676082 0.1989149962111156 chr18 78077248 2459307 0.03149838221756996 0.5846055429748589 chr19 59128983 1462456 0.02473331902224667 0.375363984166442 chr20 63025520 1670884 0.026511229102116094 0.18534100139129067 chr21 48129895 1159727 0.024095772492335583 0.1867473409296373 chr22 51304566 856361 0.016691711221180586 0.1373356144632053 chrMT 16571 143311 8.648301249170236 6.708903186924044 chrX 155270560 5360239 0.034521927402078025 0.22418446114349347 chrY 59373566 260175 0.0043820005690747964 0.1172005447681203