BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124785.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 181,669 number of mapped reads = 175,614 (96.67%) number of supplementary alignments = 7,177 (3.95%) number of secondary alignments = 0 number of mapped bases = 23,498,205 bp number of sequenced bases = 23,481,088 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,826 duplication rate = 1.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8468 >>>>>>> ACTG content number of A's = 6,905,263 bp (29.41%) number of C's = 4,474,224 bp (19.05%) number of T's = 6,509,946 bp (27.72%) number of G's = 5,591,655 bp (23.81%) number of N's = 0 bp (0%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 295,164 number of insertions = 3,826 mapped reads with insertion percentage = 2% number of deletions = 8,921 mapped reads with deletion percentage = 4.9% homopolymer indels = 46.57% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 7.1124X There is a 0.49% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 8068223 0.03236992135718691 25.05241146121896 chr2 243199373 1748604 0.0071900020893557156 0.37757332722473413 chr3 198022430 1287263 0.006500591877394899 0.2542489446514722 chr4 191154276 1010949 0.005288654908248037 0.08806442532159346 chr5 180915260 869584 0.004806581821787725 0.24204738822582356 chr6 171115067 907838 0.005305424098042751 0.12404470241032635 chr7 159138663 908382 0.0057081163236868465 0.08374874502213567 chr8 146364022 990433 0.006766915711020841 0.18570821946992944 chr9 141213431 714592 0.005060368514096934 0.15292822212199228 chr10 135534747 870081 0.006419615775724287 0.19595425645637313 chr11 135006516 655682 0.004856669288466047 0.09138716460894374 chr12 133851895 580280 0.004335239332995622 0.07593108219687873 chr13 115169878 513158 0.004455661574982305 0.17533635104960368 chr14 107349540 558975 0.005207055381886126 0.8068031872474187 chr15 102531392 486262 0.00474256703742011 0.2474177648755894 chr16 90354753 591943 0.006551321102056469 0.11438976732990468 chr17 81195210 354622 0.00436752365071782 0.08418932894128313 chr18 78077248 343569 0.004400372820517444 0.08824920122107069 chr19 59128983 288541 0.004879857311261383 0.11372062344918456 chr20 63025520 381666 0.006055737421920517 0.0874699170302929 chr21 48129895 180836 0.003757249002932585 0.07122348033934543 chr22 51304566 151798 0.0029587619940104355 0.05810661943257778 chrMT 16571 124805 7.531530987870376 5.039921099328789 chrX 155270560 654659 0.004216246788831058 0.06701273499875708 chrY 59373566 255460 0.004302588124823091 0.13743080455665788