BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068078.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 = 2,566,952 number of mapped reads = 2,326,519 (90.63%) number of supplementary alignments = 22,729 (0.89%) number of secondary alignments = 0 number of mapped bases = 153,860,325 bp number of sequenced bases = 153,793,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,545 duplication rate = 5.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0437 >>>>>>> ACTG content number of A's = 42,707,488 bp (27.77%) number of C's = 28,566,337 bp (18.57%) number of T's = 48,475,366 bp (31.52%) number of G's = 34,040,876 bp (22.13%) number of N's = 3,072 bp (0%) GC percentage = 40.71% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,186,114 number of insertions = 12,051 mapped reads with insertion percentage = 0.51% number of deletions = 41,467 mapped reads with deletion percentage = 1.76% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.4976X There is a 3.77% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 15404176 0.06180195635299942 1.0073482187610336 chr2 243199373 15255140 0.06272688869144412 0.5499380259347848 chr3 198022430 11389593 0.0575166813173639 0.30083708307999574 chr4 191154276 6286609 0.0328876190036157 0.24794146323536423 chr5 180915260 6245135 0.03451966959558857 0.23584553951120693 chr6 171115067 11927690 0.06970566770721599 0.36395081195830076 chr7 159138663 9381929 0.05895442894351827 0.6291910123024211 chr8 146364022 5583068 0.03814508458916222 0.859915683323529 chr9 141213431 5772650 0.04087890195090579 0.3832132565493162 chr10 135534747 8718955 0.06433003486552419 0.40534231097808915 chr11 135006516 4881900 0.03616047687653832 0.31088718671315135 chr12 133851895 6974677 0.0521074206681945 0.3006266864138757 chr13 115169878 4787762 0.04157130391333748 0.2571772738511274 chr14 107349540 4080011 0.03800678605609302 0.2765086658096177 chr15 102531392 3533244 0.03446011929692713 0.24086768762414495 chr16 90354753 4512416 0.04994110271099961 0.30195015047984886 chr17 81195210 5115339 0.06300050212321638 0.32069848703828485 chr18 78077248 3683757 0.047180927790897546 0.7166686272443976 chr19 59128983 4389545 0.0742367748824633 0.6918478494668199 chr20 63025520 2305872 0.036586322492856864 0.24915574953251488 chr21 48129895 2994427 0.06221553153190964 0.3286361846908072 chr22 51304566 2460844 0.04796539941493706 0.2719011180514037 chrMT 16571 16451 0.9927584334077606 1.5374362894663682 chrX 155270560 7826725 0.05040701212129331 0.32977766153858806 chrY 59373566 332410 0.00559861942602538 0.13312727242006195