BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716329.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 = 490,552 number of mapped reads = 443,890 (90.49%) number of supplementary alignments = 1,613 (0.33%) number of secondary alignments = 0 number of mapped bases = 25,699,870 bp number of sequenced bases = 25,692,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,115 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8455 >>>>>>> ACTG content number of A's = 6,531,909 bp (25.42%) number of C's = 4,734,788 bp (18.43%) number of T's = 8,274,092 bp (32.2%) number of G's = 6,151,447 bp (23.94%) number of N's = 405 bp (0%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 136,427 number of insertions = 1,611 mapped reads with insertion percentage = 0.36% number of deletions = 4,335 mapped reads with deletion percentage = 0.97% homopolymer indels = 43.36% >>>>>>> Coverage mean coverageData = 0.0083X std coverageData = 0.1091X There is a 0.79% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 2096936 0.008412961988166922 0.16257738794448326 chr2 243199373 2231964 0.009177507213392364 0.11598633174930877 chr3 198022430 1747053 0.00882250056218379 0.09690287176191975 chr4 191154276 1728386 0.009041838017790405 0.10125916102523848 chr5 180915260 1538054 0.0085015161241788 0.09522911958665621 chr6 171115067 1485406 0.008680743467201518 0.09893103073789106 chr7 159138663 1402108 0.00881060562887851 0.1186931151070535 chr8 146364022 1311694 0.008961860859494556 0.11696019278484694 chr9 141213431 1072527 0.007595077836470102 0.10030232945535326 chr10 135534747 1210591 0.008931960451440544 0.10993415476683664 chr11 135006516 1159236 0.00858651889068821 0.10631459039145094 chr12 133851895 1172147 0.0087570444930944 0.09742118385481972 chr13 115169878 832526 0.0072286783181275925 0.08748193354156959 chr14 107349540 768852 0.007162135953260722 0.08799155931793858 chr15 102531392 727200 0.007092461984715861 0.08665004386187868 chr16 90354753 701436 0.0077631333904482035 0.09318653780076798 chr17 81195210 645253 0.007946934308070636 0.09378006559078152 chr18 78077248 687718 0.008808174181549023 0.14737849055034796 chr19 59128983 474116 0.008018335103108403 0.13333746939698818 chr20 63025520 521510 0.008274584644442442 0.09432860067917703 chr21 48129895 345824 0.007185222406988422 0.0896707279387365 chr22 51304566 271870 0.0052991384821382175 0.07471230016946895 chrMT 16571 2989 0.1803753545350311 0.4196214910143745 chrX 155270560 1484830 0.009562855959300978 0.10430745877135078 chrY 59373566 79644 0.0013414050286283967 0.04594024130008475