BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068141.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 = 2,830,764 number of mapped reads = 2,462,083 (86.98%) number of supplementary alignments = 23,039 (0.81%) number of secondary alignments = 0 number of mapped bases = 165,596,017 bp number of sequenced bases = 165,505,249 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,670 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1018 >>>>>>> ACTG content number of A's = 46,898,680 bp (28.34%) number of C's = 30,122,794 bp (18.2%) number of T's = 52,941,350 bp (31.99%) number of G's = 35,538,787 bp (21.47%) number of N's = 3,638 bp (0%) GC percentage = 39.67% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,342,475 number of insertions = 12,902 mapped reads with insertion percentage = 0.52% number of deletions = 55,837 mapped reads with deletion percentage = 2.24% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.6139X There is a 4.41% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 19697028 0.079024990673945 1.3224941135391113 chr2 243199373 13868402 0.05702482629344608 0.5379900830372737 chr3 198022430 9582604 0.04839150797210195 0.25714841234818614 chr4 191154276 11603543 0.060702502935377704 0.29020273796277274 chr5 180915260 7819827 0.043223700421954454 0.24385391894254785 chr6 171115067 8762481 0.05120812067355822 0.33631970196406774 chr7 159138663 15562416 0.09779154673430931 1.2598739603603863 chr8 146364022 7637558 0.05218193580386852 0.8161128277156179 chr9 141213431 4626028 0.03275912189967256 0.4529718233414031 chr10 135534747 9350835 0.06899216036460377 0.39650463410574943 chr11 135006516 7092608 0.052535301333159354 0.4217245673345039 chr12 133851895 5352079 0.03998508201919741 0.2601874906575462 chr13 115169878 3970444 0.03447467401155014 0.21663661664784972 chr14 107349540 3219641 0.029992126654664754 0.26436509276553255 chr15 102531392 4065885 0.039655025848083676 0.23484437128462515 chr16 90354753 2157273 0.023875589588518934 0.2188391707935758 chr17 81195210 5032494 0.06198018331376937 0.3280708184205886 chr18 78077248 2541108 0.032546075394460625 0.7946382168729096 chr19 59128983 3657471 0.0618558076671131 0.8995162346162839 chr20 63025520 1384026 0.021959771216485006 0.2118939759235315 chr21 48129895 2712741 0.05636291124258634 0.2855688112028337 chr22 51304566 1804813 0.035178408876901913 0.2133306193423451 chrMT 16571 18879 1.1392794641240722 1.439457110832364 chrX 155270560 13731721 0.0884373766668968 0.4209434279748201 chrY 59373566 344112 0.0057957105018755315 0.11737085481444534