BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081970.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,962,015 number of mapped reads = 2,742,993 (92.61%) number of supplementary alignments = 17,442 (0.59%) number of secondary alignments = 0 number of mapped bases = 186,858,218 bp number of sequenced bases = 186,788,878 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,773 duplication rate = 4.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9942 >>>>>>> ACTG content number of A's = 53,256,228 bp (28.51%) number of C's = 34,184,862 bp (18.3%) number of T's = 59,595,170 bp (31.91%) number of G's = 39,728,453 bp (21.27%) number of N's = 24,165 bp (0.01%) GC percentage = 39.57% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,391,489 number of insertions = 12,888 mapped reads with insertion percentage = 0.47% number of deletions = 39,400 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.67% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.4391X There is a 5.04% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 17108121 0.06863822818720279 0.7003151530713964 chr2 243199373 16481326 0.06776878491376703 0.5637099028133472 chr3 198022430 12011272 0.06065611860232197 0.28355655195807106 chr4 191154276 9610150 0.05027431350790186 0.26813693354832013 chr5 180915260 9571537 0.052906189339694175 0.266429135753218 chr6 171115067 16513122 0.0965030274043606 0.4475733324634755 chr7 159138663 12128225 0.07621168087858071 0.5610683049064641 chr8 146364022 10475679 0.07157277353310228 0.7017459266014514 chr9 141213431 8980929 0.06359826353911052 0.4430280548807705 chr10 135534747 7466532 0.05508943031413192 0.4316998075526603 chr11 135006516 8509656 0.06303144657106773 0.35147130172216057 chr12 133851895 7914927 0.05913197568103164 0.28568025817755927 chr13 115169878 5146888 0.044689532448753656 0.2415532797621978 chr14 107349540 4616147 0.043001087848164046 0.2564732227217307 chr15 102531392 4354287 0.04246784243405181 0.23805240882433254 chr16 90354753 3845022 0.042554728692579126 0.2755511066386392 chr17 81195210 5049597 0.0621908238183016 0.30952861653420904 chr18 78077248 5305524 0.06795224134949018 0.6882003317108312 chr19 59128983 3717218 0.06286625968182134 0.5387728934012691 chr20 63025520 4730862 0.07506264129197189 0.3197554813895959 chr21 48129895 2021867 0.04200854790977624 0.2524179824992139 chr22 51304566 1437644 0.028021755412568933 0.18848475339857637 chrMT 16571 114359 6.901152616015931 4.141289875536321 chrX 155270560 9355978 0.06025596867815766 0.31308322655094245 chrY 59373566 391349 0.0065913002429397625 0.13286195242475174