BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008805.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 = 1,527,159 number of mapped reads = 1,290,099 (84.48%) number of supplementary alignments = 9,550 (0.63%) number of secondary alignments = 0 number of mapped bases = 84,175,528 bp number of sequenced bases = 84,128,546 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,946 duplication rate = 6.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.58 >>>>>>> ACTG content number of A's = 22,534,925 bp (26.79%) number of C's = 16,412,156 bp (19.51%) number of T's = 25,811,289 bp (30.68%) number of G's = 19,244,101 bp (22.87%) number of N's = 126,075 bp (0.15%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 730,579 number of insertions = 6,114 mapped reads with insertion percentage = 0.47% number of deletions = 26,293 mapped reads with deletion percentage = 2.01% homopolymer indels = 45.43% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.3111X There is a 1.82% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6536969 0.026226490324371146 0.5236041105443985 chr2 243199373 8225804 0.03382329443752308 0.41009147777798916 chr3 198022430 7970766 0.040251834097783774 0.28382812912562655 chr4 191154276 4903362 0.025651333062515432 0.22560883623187242 chr5 180915260 3380717 0.01868674317467747 0.1907852033237448 chr6 171115067 4145844 0.024228398309308438 0.23414145299793487 chr7 159138663 2839743 0.017844456818139787 0.22572050973949376 chr8 146364022 6094714 0.04164079339115182 0.4165010058842374 chr9 141213431 2232599 0.01581010378538285 0.2228980879497882 chr10 135534747 5890313 0.04345980001718674 0.39298554576852374 chr11 135006516 2072487 0.015351014613250223 0.1903711884927839 chr12 133851895 5507537 0.04114650001779952 0.28855234173745586 chr13 115169878 2831947 0.024589302768906293 0.22066900429349326 chr14 107349540 1894257 0.01764569275285204 0.19227616020889135 chr15 102531392 1868512 0.01822380408138807 0.1864001885807956 chr16 90354753 1730996 0.019157774688399624 0.25710951298455814 chr17 81195210 3982685 0.049050738337889636 0.3264108571766392 chr18 78077248 1753493 0.022458437571979996 0.3533850461539483 chr19 59128983 2532370 0.042827897107582585 0.46054562561275725 chr20 63025520 2420097 0.03839868358087327 0.281721233486906 chr21 48129895 858050 0.017827797047967796 0.1946188757931307 chr22 51304566 1013767 0.01975978122493035 0.1966144068403876 chrMT 16571 218844 13.206444994267093 8.655253385049132 chrX 155270560 3061127 0.019714793325920896 0.20223432025707958 chrY 59373566 208528 0.003512135349929967 0.16063285440303204