BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084260.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 = 2,233,923 number of mapped reads = 1,841,020 (82.41%) number of supplementary alignments = 13,953 (0.62%) number of secondary alignments = 0 number of mapped bases = 116,589,641 bp number of sequenced bases = 116,551,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,408 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0335 >>>>>>> ACTG content number of A's = 33,518,784 bp (28.76%) number of C's = 21,886,829 bp (18.78%) number of T's = 35,664,453 bp (30.6%) number of G's = 25,480,229 bp (21.86%) number of N's = 1,227 bp (0%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 966,048 number of insertions = 8,680 mapped reads with insertion percentage = 0.47% number of deletions = 24,326 mapped reads with deletion percentage = 1.31% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.2779X There is a 3.34% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9044623 0.036287263653397274 0.4105067168392013 chr2 243199373 9415876 0.038716695211216685 0.3257715673778801 chr3 198022430 7589369 0.03832580480908147 0.21501742320934114 chr4 191154276 8543902 0.04469636870691818 0.23726422716895412 chr5 180915260 7632849 0.04219018893154729 0.22572873595272358 chr6 171115067 7265323 0.04245869827465281 0.26103203180726564 chr7 159138663 6271535 0.039409247770292 0.3261916143591822 chr8 146364022 5836733 0.039878194929625535 0.31538867713623625 chr9 141213431 5098508 0.036104979277785554 0.2643375692593943 chr10 135534747 5291998 0.03904532318933683 0.286116354164902 chr11 135006516 5369872 0.0397749098273153 0.25560770056832166 chr12 133851895 5012182 0.03744573059649249 0.21485598949147885 chr13 115169878 3609368 0.03133951396562216 0.19526130860878152 chr14 107349540 3628830 0.03380387098072334 0.21107856995600222 chr15 102531392 3694784 0.036035636773564916 0.21238507609789703 chr16 90354753 3229769 0.035745424482539395 0.22710356532746012 chr17 81195210 2878000 0.03544544068547886 0.2292670406136166 chr18 78077248 3014106 0.038604152646363764 0.4608772800475308 chr19 59128983 1828905 0.030930770448055905 0.33432342114983044 chr20 63025520 2231465 0.035405737231521454 0.21239711789195187 chr21 48129895 1509412 0.03136121531119068 0.2032106187862465 chr22 51304566 1135115 0.022125028793733487 0.16310854694157936 chrMT 16571 59331 3.5804115623679924 2.641890699409277 chrX 155270560 7108982 0.04578448097308337 0.2514069640352805 chrY 59373566 288804 0.00486418484616538 0.10190917139754245