BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549016.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,536,316 number of mapped reads = 7,437,405 (87.13%) number of secondary alignments = 0 number of mapped bases = 293,687,787 bp number of sequenced bases = 293,657,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,238 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.2284 >>>>>>> ACTG content number of A's = 84,756,958 bp (28.86%) number of C's = 61,843,485 bp (21.06%) number of T's = 85,566,965 bp (29.14%) number of G's = 61,480,121 bp (20.94%) number of N's = 9,880 bp (0%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 897,668 number of insertions = 10,695 mapped reads with insertion percentage = 0.14% number of deletions = 23,608 mapped reads with deletion percentage = 0.32% homopolymer indels = 38.88% >>>>>>> Coverage mean coverageData = 0.0949X std coverageData = 1.192X There is a 7.73% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.22% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 23002726 0.09228753736986678 1.4295435269700365 chr2 243199373 24758584 0.1018036506204315 0.8027701480528979 chr3 198022430 19559471 0.09877401767062448 0.3781443047109793 chr4 191154276 19402521 0.1015018936850777 0.390011279094774 chr5 180915260 18159173 0.10037391539000082 0.4005032356126293 chr6 171115067 17258852 0.10086108898873294 0.4605803252764127 chr7 159138663 16519632 0.10380652751870864 1.1500727484030977 chr8 146364022 15602099 0.10659791106314365 4.272369396264967 chr9 141213431 12261542 0.08682985685688778 0.7925102946481456 chr10 135534747 13289645 0.09805341651613515 0.6409397851910282 chr11 135006516 13373838 0.0990606853375877 0.7765378079293572 chr12 133851895 13538110 0.10114246047842655 0.42016512164649344 chr13 115169878 9496735 0.082458496656565 0.32999904612626313 chr14 107349540 8951985 0.08339099543416767 0.5211661035243245 chr15 102531392 8146313 0.07945189118275113 0.33223500453686183 chr16 90354753 7957910 0.08807406069717218 0.43991881756959283 chr17 81195210 7518966 0.09260356614632809 0.41807245749520855 chr18 78077248 7833149 0.10032562879265416 1.545195096964065 chr19 59128983 6155598 0.10410458099710594 1.4499931553834078 chr20 63025520 5785648 0.0917984968628581 0.392309047946405 chr21 48129895 3679375 0.07644676972596762 0.4397734019882132 chr22 51304566 3057674 0.059598477063425505 0.35518286145191347 chrMT 16571 25721 1.5521694526582583 1.9947392316899364 chrX 155270560 17329729 0.11160988277494459 0.5909586284330909 chrY 59373566 1022791 0.017226369728238995 0.21247368784604956