BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063603.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 = 4,762,100 number of mapped reads = 4,506,185 (94.63%) number of supplementary alignments = 32,353 (0.68%) number of secondary alignments = 0 number of mapped bases = 288,884,867 bp number of sequenced bases = 288,771,386 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 633,818 duplication rate = 11.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5447 >>>>>>> ACTG content number of A's = 73,615,582 bp (25.49%) number of C's = 52,641,568 bp (18.23%) number of T's = 93,577,133 bp (32.41%) number of G's = 68,904,761 bp (23.86%) number of N's = 32,342 bp (0.01%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,494,594 number of insertions = 17,957 mapped reads with insertion percentage = 0.4% number of deletions = 64,640 mapped reads with deletion percentage = 1.42% homopolymer indels = 44.6% >>>>>>> Coverage mean coverageData = 0.0933X std coverageData = 0.9845X There is a 6.54% of reference with a coverageData >= 1X There is a 1.78% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 27711534 0.11117939802444865 2.0857881274276093 chr2 243199373 28933756 0.11897134290720396 1.736436291158267 chr3 198022430 17401874 0.08787829742317575 0.4011806006128581 chr4 191154276 13761944 0.07199391134729312 0.4004064929731358 chr5 180915260 14348636 0.07931136378434854 0.38390540967243086 chr6 171115067 19058901 0.1113806126727578 0.6602220013428787 chr7 159138663 26732087 0.1679798390665127 1.414997142725781 chr8 146364022 11046103 0.0754700700968712 0.8751260318090849 chr9 141213431 9510337 0.06734725537544654 0.6500304771943078 chr10 135534747 15126659 0.11160723972871694 0.65234505529607 chr11 135006516 13898577 0.10294745329181 0.5521803447538286 chr12 133851895 11557429 0.08634490382074904 0.4319199735912692 chr13 115169878 6579336 0.05712722904855382 0.37492937296641315 chr14 107349540 6293171 0.05862317621482123 0.38351595144575146 chr15 102531392 5451467 0.053168760256371045 0.35722722709578214 chr16 90354753 6612272 0.07318123043289156 0.40799605294234204 chr17 81195210 9805323 0.12076233314748493 0.5083450216520201 chr18 78077248 6583433 0.08431948062513679 1.2491091195513353 chr19 59128983 7013480 0.11861323574599618 1.3157712245106317 chr20 63025520 4588800 0.07280860197583455 0.39626721440319185 chr21 48129895 4974851 0.1033630137776116 0.4575973931354836 chr22 51304566 3672472 0.07158177695139259 0.3574523126411875 chrMT 16571 397833 24.00778468408666 13.148926744684758 chrX 155270560 17035286 0.10971356063892601 0.5573605553490252 chrY 59373566 789306 0.013293895805416168 0.41369656248933845