BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714139.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 659,508 number of mapped reads = 591,361 (89.67%) number of supplementary alignments = 19,328 (2.93%) number of secondary alignments = 0 number of mapped bases = 76,364,782 bp number of sequenced bases = 74,864,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 509,633 duplication rate = 43.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5447 >>>>>>> ACTG content number of A's = 21,256,658 bp (28.39%) number of C's = 15,949,547 bp (21.3%) number of T's = 20,115,618 bp (26.87%) number of G's = 17,542,055 bp (23.43%) number of N's = 517 bp (0%) GC percentage = 44.74% >>>>>>> Mismatches and indels general error rate = 0.0435 number of mismatches = 2,964,262 number of insertions = 88,562 mapped reads with insertion percentage = 14.57% number of deletions = 255,497 mapped reads with deletion percentage = 41.04% homopolymer indels = 27.92% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 2.7482X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6640724 0.026642758093669904 2.80046172726409 chr2 243199373 7263636 0.0298670013429681 4.819063935597441 chr3 198022430 4179212 0.021104740508436342 2.04399314484489 chr4 191154276 3811709 0.019940485139866817 2.242516113618884 chr5 180915260 4093757 0.02262803591029303 2.1904262279982443 chr6 171115067 2859830 0.0167129058249441 1.5759473706841536 chr7 159138663 3222274 0.02024821585939804 2.165863310296758 chr8 146364022 3750960 0.02562760949545374 2.676427825602431 chr9 141213431 2937590 0.020802483015939184 2.4270878634890884 chr10 135534747 4118740 0.030388812398048744 2.779354599508808 chr11 135006516 3656444 0.027083463141882723 2.6762285444323566 chr12 133851895 3515162 0.026261578142020327 2.7847679775207115 chr13 115169878 1911041 0.016593236297428395 1.6794213931527386 chr14 107349540 2737718 0.025502838670757227 2.817080430063299 chr15 102531392 2401583 0.023422904470076833 2.2760817481395312 chr16 90354753 2513203 0.027814840022859673 3.1145930912049917 chr17 81195210 2870481 0.03535283670058862 3.665387793375179 chr18 78077248 1774272 0.022724571439813043 2.2670445929912577 chr19 59128983 1592536 0.02693325538847844 3.053140229680103 chr20 63025520 1904191 0.030213015299199435 2.5780806041411237 chr21 48129895 771574 0.01603107590407168 1.7188860360422975 chr22 51304566 843647 0.016443897020783686 1.7715956951681038 chrMT 16571 227946 13.755717820288456 124.89007782279755 chrX 155270560 6449208 0.041535291686975305 2.957321156122541 chrY 59373566 317344 0.005344870139684721 0.8996250825668783