BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004052.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 = 5,191,351 number of mapped reads = 4,604,259 (88.69%) number of supplementary alignments = 34,272 (0.66%) number of secondary alignments = 0 number of mapped bases = 305,415,710 bp number of sequenced bases = 305,286,740 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,440 duplication rate = 5.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6927 >>>>>>> ACTG content number of A's = 84,617,150 bp (27.72%) number of C's = 57,727,603 bp (18.91%) number of T's = 94,336,403 bp (30.9%) number of G's = 68,298,121 bp (22.37%) number of N's = 307,463 bp (0.1%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,499,866 number of insertions = 21,211 mapped reads with insertion percentage = 0.46% number of deletions = 74,226 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.0987X std coverageData = 0.7988X There is a 7.25% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% 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% 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 26039361 0.10447059628389051 1.4747660004512797 chr2 243199373 24563586 0.10100184756644089 0.9064635712552511 chr3 198022430 24272063 0.12257229143183426 0.44552585926706556 chr4 191154276 21669037 0.11335889237445047 0.45351586345259015 chr5 180915260 13752937 0.07601866752423206 0.35682059002996613 chr6 171115067 15983868 0.09341005605310022 0.4467606272425661 chr7 159138663 21592092 0.13568099412774381 1.4814258439315902 chr8 146364022 17776778 0.12145592719500425 1.1123922146100278 chr9 141213431 8429618 0.0596941660598842 0.6411430442442437 chr10 135534747 14388427 0.10616042984165529 0.6860540441076866 chr11 135006516 11734412 0.08691737515839607 0.5362898039670416 chr12 133851895 14054489 0.10500029902453006 0.42899077283400094 chr13 115169878 9747116 0.08463251128910634 0.379503969633281 chr14 107349540 9698113 0.09034144906443009 0.439197333226455 chr15 102531392 6949489 0.06777913441378032 0.344490881765708 chr16 90354753 8251618 0.09132466999273409 0.4498928734911633 chr17 81195210 7699429 0.0948261479956761 0.4559358439159835 chr18 78077248 8197768 0.10499560640252074 1.4443712973897973 chr19 59128983 5755179 0.09733262281882982 1.0033360940281626 chr20 63025520 8533674 0.1354002949916161 0.5173087038767108 chr21 48129895 3133075 0.06509623592571727 0.35918334307427174 chr22 51304566 4037535 0.07869738143774571 0.3559033725341642 chrMT 16571 51832 3.127873996741295 2.984285724373307 chrX 155270560 18377808 0.1183599002927535 0.5160939899511401 chrY 59373566 726406 0.012234501798325538 0.18707076891061222