BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174092.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,532,412 number of mapped reads = 2,490,655 (98.35%) number of supplementary alignments = 268,361 (10.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,244,619 number of mapped paired reads (second in pair) = 1,246,036 number of mapped paired reads (both in pair) = 2,464,708 number of mapped paired reads (singletons) = 25,947 number of mapped bases = 286,147,736 bp number of sequenced bases = 285,979,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,977,679 duplication rate = 66.81% >>>>>>> Insert size mean insert size = 879,948.327 std insert size = 8,617,376.7806 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 52.9918 >>>>>>> ACTG content number of A's = 85,703,800 bp (29.97%) number of C's = 56,687,552 bp (19.82%) number of T's = 84,977,165 bp (29.71%) number of G's = 58,608,776 bp (20.49%) number of N's = 2,288 bp (0%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 2,240,148 number of insertions = 30,077 mapped reads with insertion percentage = 1.16% number of deletions = 69,755 mapped reads with deletion percentage = 2.73% homopolymer indels = 42.27% >>>>>>> Coverage mean coverageData = 0.0924X std coverageData = 1.7559X There is a 1.95% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 1.12% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.57% of reference with a coverageData >= 6X There is a 0.42% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.27% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.17% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 22019950 0.08834461439516333 1.0136137235123048 chr2 243199373 24974482 0.10269139139598028 5.262117476463497 chr3 198022430 20542961 0.1037405762569422 0.9758915997422338 chr4 191154276 19531952 0.1021789959854207 1.0948377190170844 chr5 180915260 18062499 0.09983955471749592 0.950438594548028 chr6 171115067 16526607 0.09658183402400211 0.9929821780948961 chr7 159138663 15438930 0.09701558193938076 1.08139602457469 chr8 146364022 15131683 0.1033838971711231 1.2043467751532058 chr9 141213431 12253928 0.08677593847287798 1.0012809693151774 chr10 135534747 14764549 0.1089355263266917 1.2553677851639078 chr11 135006516 13089790 0.09695672762935383 0.9420285658148095 chr12 133851895 13799229 0.1030932658816672 0.9762944664121609 chr13 115169878 10043670 0.08720743804208944 0.9003141399648521 chr14 107349540 8615016 0.08025200666905513 0.8494552840049473 chr15 102531392 8271606 0.08067388766164416 0.8483393737189379 chr16 90354753 8651273 0.09574784626991344 1.015581407303366 chr17 81195210 7783185 0.09585768667880777 0.9385890869111598 chr18 78077248 8167882 0.10461283164078734 1.178050865632226 chr19 59128983 4919322 0.08319645883305654 0.8886892024580033 chr20 63025520 5850701 0.09283066605400479 0.9184737517067073 chr21 48129895 4019121 0.08350570887387143 0.9601532737348236 chr22 51304566 3357761 0.06544760557958916 0.8059192327019089 chrMT 16571 242633 14.642025224790297 19.46278043649464 chrX 155270560 7987546 0.05144275901368553 0.6827366483946016 chrY 59373566 2101460 0.0353938653440489 0.6541667352037629