BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234150.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 = 757,250 number of mapped reads = 466,739 (61.64%) number of supplementary alignments = 4,043 (0.53%) number of secondary alignments = 0 number of mapped bases = 29,845,617 bp number of sequenced bases = 29,817,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,001 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2699 >>>>>>> ACTG content number of A's = 8,452,408 bp (28.35%) number of C's = 5,010,515 bp (16.8%) number of T's = 10,000,921 bp (33.54%) number of G's = 6,349,995 bp (21.3%) number of N's = 4,148 bp (0.01%) GC percentage = 38.1% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 287,466 number of insertions = 2,612 mapped reads with insertion percentage = 0.55% number of deletions = 15,662 mapped reads with deletion percentage = 3.28% homopolymer indels = 42.32% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 0.1483X There is a 0.83% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2563665 0.01028549092361138 0.20065692277058852 chr2 243199373 1660413 0.006827373687349103 0.10832307183113105 chr3 198022430 3212777 0.016224308529089355 0.14558109029007751 chr4 191154276 1524548 0.007975484681284346 0.104770924136117 chr5 180915260 2001807 0.011064887505896407 0.1205672728679317 chr6 171115067 2216976 0.012956053717934728 0.14063490298966705 chr7 159138663 1603224 0.01007438399806086 0.12716952165188622 chr8 146364022 1786787 0.012207829325706833 0.365954239650251 chr9 141213431 1147479 0.008125848879063069 0.11010978533754985 chr10 135534747 1710267 0.01261866080732788 0.14026755328685814 chr11 135006516 1360700 0.010078772790492572 0.12208812905893905 chr12 133851895 826508 0.006174794910449344 0.09367189134897036 chr13 115169878 1446779 0.01256213017782306 0.1300802796612541 chr14 107349540 1393606 0.012981946638988858 0.13130757254032202 chr15 102531392 586320 0.005718443771835264 0.09591107405819038 chr16 90354753 617889 0.0068384781041900475 0.09514908119432101 chr17 81195210 539290 0.006641894269378699 0.09310384341440893 chr18 78077248 685987 0.008786003830462876 0.18331660630341765 chr19 59128983 705210 0.011926638413517108 0.1445165094492418 chr20 63025520 626035 0.009933039822598846 0.11406816405108956 chr21 48129895 521260 0.01083027502968789 0.11959116089929578 chr22 51304566 198730 0.003873534375088564 0.06835985381440783 chrMT 16571 10563 0.637438899281878 0.9389681583433604 chrX 155270560 816951 0.005261467466852699 0.08448103415682531 chrY 59373566 81846 0.001378492240132587 0.047350097402176806