BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231882.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 = 1,852,583 number of mapped reads = 1,413,497 (76.3%) number of supplementary alignments = 7,795 (0.42%) number of secondary alignments = 0 number of mapped bases = 89,325,224 bp number of sequenced bases = 89,275,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,075 duplication rate = 9.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0671 >>>>>>> ACTG content number of A's = 23,597,391 bp (26.43%) number of C's = 14,964,965 bp (16.76%) number of T's = 30,179,331 bp (33.8%) number of G's = 20,530,164 bp (23%) number of N's = 4,055 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 712,234 number of insertions = 7,755 mapped reads with insertion percentage = 0.54% number of deletions = 27,669 mapped reads with deletion percentage = 1.93% homopolymer indels = 48.85% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2754X There is a 2% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 7485095 0.030030396594277694 0.2704641800560234 chr2 243199373 7035602 0.02892935912297767 0.3842884669638971 chr3 198022430 7735537 0.039063943412874995 0.27277122353003 chr4 191154276 5208651 0.027248414783041526 0.2395048919195834 chr5 180915260 4973848 0.027492694646101164 0.22778366293745672 chr6 171115067 5851398 0.03419569125376902 0.27803009511956517 chr7 159138663 5696730 0.0357972719677807 0.3332328159193145 chr8 146364022 4634031 0.03166099794661286 0.42612107159871093 chr9 141213431 3993729 0.02828150956830728 0.24735494907862737 chr10 135534747 3665795 0.027046901854621826 0.23484446895068162 chr11 135006516 4171948 0.030901826990335786 0.29003946576719364 chr12 133851895 3525100 0.026335824382613334 0.22429864977187136 chr13 115169878 3247057 0.028193630629703367 0.23396128156460824 chr14 107349540 3062054 0.028524146447204152 0.23480410531912377 chr15 102531392 2349248 0.022912475429963927 0.2132311983485124 chr16 90354753 2452948 0.02714796862982958 0.2253683123345242 chr17 81195210 2079389 0.025609749639172064 0.22789158543475113 chr18 78077248 2366679 0.030312018681805997 0.3373785710197764 chr19 59128983 1917809 0.032434330893193274 0.25613805858643485 chr20 63025520 2261005 0.03587443626010543 0.2658515430627497 chr21 48129895 1325026 0.02753020757680855 0.2298292827529561 chr22 51304566 808043 0.015749923700748195 0.1697550381908077 chrMT 16571 35247 2.127029147305534 2.478203240400924 chrX 155270560 3017855 0.019436105595291214 0.1942562286421942 chrY 59373566 425400 0.007164804620291798 0.11911356366356786