BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716452.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 = 603,874 number of mapped reads = 486,395 (80.55%) number of supplementary alignments = 6,989 (1.16%) number of secondary alignments = 0 number of mapped bases = 38,032,230 bp number of sequenced bases = 38,015,880 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,600 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6221 >>>>>>> ACTG content number of A's = 9,724,248 bp (25.58%) number of C's = 6,975,879 bp (18.35%) number of T's = 11,765,039 bp (30.95%) number of G's = 9,548,386 bp (25.12%) number of N's = 2,328 bp (0.01%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 318,188 number of insertions = 3,471 mapped reads with insertion percentage = 0.7% number of deletions = 9,347 mapped reads with deletion percentage = 1.89% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.0123X std coverageData = 0.1629X There is a 1.14% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% 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 3103990 0.012453288932828778 0.22828209735329244 chr2 243199373 3316620 0.01363745292221621 0.2303716160887556 chr3 198022430 2532620 0.012789561263337693 0.1180185119175207 chr4 191154276 2520537 0.013185878196101666 0.12567896215847218 chr5 180915260 2396044 0.013244012694119888 0.12148496622007668 chr6 171115067 2220022 0.01297385460510032 0.1287045568292339 chr7 159138663 2146170 0.013486163321605888 0.20114447081109602 chr8 146364022 2019527 0.013797974204343743 0.19980762122134205 chr9 141213431 1652689 0.01170348307732853 0.17100468575241776 chr10 135534747 1846000 0.013620123553999035 0.15354867964972782 chr11 135006516 1747843 0.012946360307527676 0.1625462227842503 chr12 133851895 1774857 0.013259857098026143 0.12126612780152686 chr13 115169878 1202885 0.010444441036917657 0.10647002692551531 chr14 107349540 1164414 0.010846939819211148 0.12682783867113842 chr15 102531392 1083145 0.010564032915889799 0.10864386751839522 chr16 90354753 1160434 0.01284308751306088 0.12632436846185457 chr17 81195210 1115163 0.013734344673780633 0.12732368090872204 chr18 78077248 1071155 0.013719169507613793 0.29355575468410366 chr19 59128983 852569 0.01441880033688386 0.1802517170826098 chr20 63025520 801223 0.012712675754202424 0.12128689122836515 chr21 48129895 490222 0.010185395168636873 0.10938624708709035 chr22 51304566 460079 0.008967603390310329 0.09971738509206336 chrMT 16571 4803 0.28984370285438416 0.5707692934112124 chrX 155270560 1256642 0.008093240598861755 0.11098384148713973 chrY 59373566 92577 0.0015592292367953779 0.06097458841996491