BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818774.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 357,827 number of mapped reads = 312,189 (87.25%) number of supplementary alignments = 2,429 (0.68%) number of secondary alignments = 0 number of mapped bases = 21,196,511 bp number of sequenced bases = 21,187,870 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,480 duplication rate = 23.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2909 >>>>>>> ACTG content number of A's = 5,991,714 bp (28.28%) number of C's = 4,840,248 bp (22.84%) number of T's = 5,919,118 bp (27.94%) number of G's = 4,435,467 bp (20.93%) number of N's = 1,323 bp (0.01%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 105,957 number of insertions = 2,490 mapped reads with insertion percentage = 0.79% number of deletions = 5,343 mapped reads with deletion percentage = 1.69% homopolymer indels = 41.95% >>>>>>> Coverage mean coverageData = 0.0068X std coverageData = 0.1322X There is a 0.46% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 1767904 0.0070928770123304926 0.14601887607444614 chr2 243199373 1825821 0.00750750701976522 0.18514116962892277 chr3 198022430 1400345 0.007071648398618278 0.11979767902647898 chr4 191154276 1358837 0.007108588039118727 0.1239169591522944 chr5 180915260 1314933 0.007268226019187104 0.12194567769493969 chr6 171115067 1227753 0.007175013992192751 0.12589532776034706 chr7 159138663 1126516 0.007078832879223071 0.12309434551185164 chr8 146364022 1093773 0.007472963540179294 0.12533903328904672 chr9 141213431 895448 0.0063410965490952485 0.11599532198143593 chr10 135534747 1005971 0.007422236896933891 0.13818201291764837 chr11 135006516 994693 0.007367740680012808 0.12731600844438573 chr12 133851895 954915 0.007134116405300052 0.12286907121543177 chr13 115169878 693083 0.006017919025667458 0.11178366275269291 chr14 107349540 669209 0.0062339251756458386 0.11567373515169126 chr15 102531392 646011 0.006300616693080691 0.11264753016134083 chr16 90354753 684059 0.007570813679275953 0.15942232793247066 chr17 81195210 586890 0.0072281357484019065 0.12363022636605255 chr18 78077248 571120 0.007314806997295806 0.1432165485306535 chr19 59128983 447728 0.0075720564989254086 0.13654425819569463 chr20 63025520 488622 0.007752764277073795 0.13135889921657534 chr21 48129895 278969 0.00579616888838008 0.1089269435243218 chr22 51304566 275710 0.0053739856214747046 0.11129538161414497 chrMT 16571 26801 1.6173435519884134 2.524513202975092 chrX 155270560 666982 0.004295611479729319 0.09545977773129986 chrY 59373566 194418 0.003274487505096123 0.16404407200417573