BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240064.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 = 3,160,835 number of mapped reads = 2,356,498 (74.55%) number of supplementary alignments = 25,874 (0.82%) number of secondary alignments = 0 number of mapped bases = 157,031,809 bp number of sequenced bases = 156,969,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 484,677 duplication rate = 12.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5599 >>>>>>> ACTG content number of A's = 44,690,146 bp (28.47%) number of C's = 29,482,092 bp (18.78%) number of T's = 49,536,978 bp (31.56%) number of G's = 33,245,052 bp (21.18%) number of N's = 15,057 bp (0.01%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,259,323 number of insertions = 12,384 mapped reads with insertion percentage = 0.52% number of deletions = 35,688 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.33% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.7191X There is a 1.48% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% 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 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 12552766 0.05036202497565693 0.9631268442515949 chr2 243199373 12036216 0.04949114733120632 0.7038502525226362 chr3 198022430 10354547 0.052289768386338864 0.5669036129659571 chr4 191154276 9344398 0.04888406472267458 0.5674926518407869 chr5 180915260 9367788 0.05177997699033238 0.5635689162248594 chr6 171115067 8554414 0.049992172810825596 0.5811429545999244 chr7 159138663 9879546 0.06208136862378943 0.9347610721802161 chr8 146364022 12005069 0.08202199444888171 1.4068648042164007 chr9 141213431 6312721 0.04470340360188543 0.6286191222698093 chr10 135534747 6271298 0.046270776600187996 0.5823987153033855 chr11 135006516 6355447 0.04707511302639644 0.6942590584688516 chr12 133851895 7186587 0.053690588392491564 0.5754950487345167 chr13 115169878 6595995 0.05727187624528004 0.6036625127136956 chr14 107349540 3708912 0.03454986393048354 0.4741764099686997 chr15 102531392 4576062 0.0446308385240688 0.5166572546906626 chr16 90354753 3945375 0.043665384155275155 0.5192676720741696 chr17 81195210 6183066 0.076150625141557 0.7452487247594949 chr18 78077248 4272667 0.054723586056721674 1.0399298372661416 chr19 59128983 2742053 0.04637409373335577 0.6510185021131931 chr20 63025520 2749331 0.0436225040269402 0.5154335624967138 chr21 48129895 1832798 0.03808024098120306 0.48605709190560104 chr22 51304566 1454795 0.02835605314349604 0.38455292691408943 chrMT 16571 137725 8.31120632430149 7.736417318709854 chrX 155270560 8132843 0.0523785255878513 0.5923652414001459 chrY 59373566 479390 0.008074131845137953 0.2442400842341315