BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 635,854 number of mapped reads = 576,558 (90.67%) number of supplementary alignments = 2,157 (0.34%) number of secondary alignments = 0 number of mapped bases = 32,812,432 bp number of sequenced bases = 32,803,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,617 duplication rate = 1.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8958 >>>>>>> ACTG content number of A's = 7,931,808 bp (24.18%) number of C's = 6,610,186 bp (20.15%) number of T's = 10,033,176 bp (30.59%) number of G's = 8,227,432 bp (25.08%) number of N's = 798 bp (0%) GC percentage = 45.23% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 161,563 number of insertions = 2,078 mapped reads with insertion percentage = 0.36% number of deletions = 5,277 mapped reads with deletion percentage = 0.91% homopolymer indels = 40.57% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.117X There is a 1.01% of reference with a coverageData >= 1X There is a 0.04% 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 3659452 0.01468181698131055 0.15192476206577454 chr2 243199373 2733489 0.011239704141835925 0.1268208930289343 chr3 198022430 2128426 0.010748408652494568 0.10724807189378005 chr4 191154276 2051473 0.010732027778442163 0.11123687909773831 chr5 180915260 1645878 0.009097507860862594 0.09888190023072804 chr6 171115067 1694041 0.009900010733712888 0.10617212984191535 chr7 159138663 1423250 0.00894345832225573 0.10890014785702647 chr8 146364022 2039553 0.013934797446328716 0.12791997919151496 chr9 141213431 1184765 0.00838988891927709 0.1086358075401562 chr10 135534747 1581526 0.011668786307617486 0.127591726580184 chr11 135006516 1310080 0.009703827924868456 0.12014425687718998 chr12 133851895 1465930 0.010951880808261998 0.10867239655985225 chr13 115169878 982556 0.00853136268842796 0.0955282463515406 chr14 107349540 899622 0.008380306054408803 0.0958086802019441 chr15 102531392 949432 0.009259915246249657 0.09962630008520837 chr16 90354753 989638 0.010952805105891883 0.11153580184316775 chr17 81195210 770475 0.009489168141815262 0.1022149362248983 chr18 78077248 796072 0.01019595362787377 0.16923107364478873 chr19 59128983 649409 0.01098292186084107 0.12461460503161731 chr20 63025520 1115136 0.01769340419563377 0.13988413772321084 chr21 48129895 422050 0.008768978199516123 0.1026132336363063 chr22 51304566 408364 0.007959603439584696 0.09247932475451837 chrMT 16571 813 0.0490616136624223 0.24183147815766104 chrX 155270560 1818889 0.011714319829850552 0.11786739279807917 chrY 59373566 92113 0.0015514143112104804 0.047976414178014806