BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080754.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 = 8,047,515 number of mapped reads = 6,563,175 (81.56%) number of supplementary alignments = 28,503 (0.35%) number of secondary alignments = 0 number of mapped bases = 420,999,788 bp number of sequenced bases = 420,864,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 798,146 duplication rate = 9.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4902 >>>>>>> ACTG content number of A's = 129,139,975 bp (30.68%) number of C's = 84,557,688 bp (20.09%) number of T's = 112,398,223 bp (26.71%) number of G's = 93,797,203 bp (22.29%) number of N's = 971,757 bp (0.23%) GC percentage = 42.38% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 4,040,648 number of insertions = 29,089 mapped reads with insertion percentage = 0.44% number of deletions = 71,487 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.136X std coverageData = 0.8452X There is a 8.07% of reference with a coverageData >= 1X There is a 2.87% of reference with a coverageData >= 2X There is a 1.21% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 53329837 0.21396069861747707 1.3328821100374106 chr2 243199373 31818306 0.1308321876306811 0.7803853545971164 chr3 198022430 25306953 0.12779841657331445 0.5632088036086743 chr4 191154276 24570614 0.12853813429734628 0.7044071714484375 chr5 180915260 32859230 0.18162774107612592 0.6761138163760746 chr6 171115067 28906034 0.16892746212699083 0.8941474665279656 chr7 159138663 29131376 0.1830565586692154 1.2934604722278316 chr8 146364022 18518311 0.12652228838040538 1.0782940028958106 chr9 141213431 14011383 0.09922131981907585 0.6206722979260415 chr10 135534747 18326358 0.1352152005714077 1.0703658709084347 chr11 135006516 14545706 0.10774077008253438 0.6966095201812529 chr12 133851895 16304179 0.12180760683291036 0.5573799762597118 chr13 115169878 17391836 0.15101028413002227 0.6159352759653159 chr14 107349540 10982573 0.10230666102528245 0.6274482135850883 chr15 102531392 10261391 0.1000804807175543 0.48731037524068493 chr16 90354753 10420696 0.11533091125820465 0.6143216396888802 chr17 81195210 10657799 0.13126142539689226 0.6012363318336729 chr18 78077248 5610067 0.07185277585603426 1.052535231598052 chr19 59128983 6725031 0.11373493435528902 1.0940688725142307 chr20 63025520 7425508 0.11781748091884049 0.5890394893467946 chr21 48129895 6621012 0.13756547775556127 0.7144406129261495 chr22 51304566 4285773 0.08353589814988396 0.45654155844093774 chrMT 16571 297718 17.966206022569548 13.19392249391273 chrX 155270560 21434003 0.1380429297092765 0.6232048523160245 chrY 59373566 1258094 0.021189463337944026 0.7008251547823194