BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716113.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 = 1,652,861 number of mapped reads = 1,233,907 (74.65%) number of supplementary alignments = 3,108 (0.19%) number of secondary alignments = 0 number of mapped bases = 67,295,653 bp number of sequenced bases = 67,278,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,596 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1598 >>>>>>> ACTG content number of A's = 15,981,296 bp (23.75%) number of C's = 14,566,199 bp (21.65%) number of T's = 19,583,264 bp (29.11%) number of G's = 17,145,880 bp (25.48%) number of N's = 1,756 bp (0%) GC percentage = 47.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 342,698 number of insertions = 5,006 mapped reads with insertion percentage = 0.4% number of deletions = 10,672 mapped reads with deletion percentage = 0.86% homopolymer indels = 36.04% >>>>>>> Coverage mean coverageData = 0.0217X std coverageData = 0.1776X There is a 1.98% of reference with a coverageData >= 1X There is a 0.15% 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 5513015 0.022118360138408642 0.19285349910588978 chr2 243199373 5649853 0.023231363347305998 0.20514360228574802 chr3 198022430 4291409 0.021671327838972586 0.16246843831383398 chr4 191154276 4045483 0.02116344496525937 0.17590654579853698 chr5 180915260 3924369 0.021691752260146545 0.16028062173863483 chr6 171115067 3726093 0.021775364760836635 0.16366497410237493 chr7 159138663 3750902 0.023570023332419227 0.21062438808603587 chr8 146364022 3275915 0.022381968978687945 0.16944548444124605 chr9 141213431 2789834 0.01975615194846445 0.1613838583941393 chr10 135534747 3271264 0.024135980421315872 0.20874792715562204 chr11 135006516 3036537 0.02249178106336734 0.18660333261609416 chr12 133851895 3095198 0.02312405065314914 0.166156271770139 chr13 115169878 1992010 0.01729627602800795 0.14341593129489438 chr14 107349540 2021151 0.018827756504592383 0.15248629035307493 chr15 102531392 1997611 0.019482920898996475 0.15375581553453282 chr16 90354753 2224731 0.024622180086088002 0.1818691590778613 chr17 81195210 2152927 0.026515443460273087 0.1815526833396448 chr18 78077248 1744151 0.022338786838388566 0.2078686376033222 chr19 59128983 1726948 0.029206455318198182 0.20773872776657587 chr20 63025520 1533689 0.024334412472915734 0.17372826963225393 chr21 48129895 868265 0.01804003520057544 0.1608367547587586 chr22 51304566 950736 0.018531216110472506 0.14955023897127936 chrMT 16571 8243 0.4974352784985819 0.7881901951595893 chrX 155270560 3483125 0.02243261697516902 0.17118512030161706 chrY 59373566 222194 0.003742305119419642 0.10840620489907005