BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084902.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 = 2,209,491 number of mapped reads = 1,997,726 (90.42%) number of supplementary alignments = 20,535 (0.93%) number of secondary alignments = 0 number of mapped bases = 132,497,578 bp number of sequenced bases = 132,445,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,792 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0509 >>>>>>> ACTG content number of A's = 35,770,224 bp (27.01%) number of C's = 24,671,122 bp (18.63%) number of T's = 41,657,747 bp (31.45%) number of G's = 30,328,406 bp (22.9%) number of N's = 18,453 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,005,146 number of insertions = 10,412 mapped reads with insertion percentage = 0.52% number of deletions = 31,031 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.0428X std coverageData = 0.3151X There is a 3.52% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 11470418 0.04601961653688317 0.39804246756060213 chr2 243199373 10866483 0.04468137752970276 0.5225564630619156 chr3 198022430 11030846 0.0557050330106544 0.27988964809133193 chr4 191154276 7630727 0.03991920641105617 0.24346130366393204 chr5 180915260 7016676 0.03878432366622915 0.2345613250074746 chr6 171115067 7715794 0.04509126014017223 0.2687473744212676 chr7 159138663 8797434 0.05528156284686142 0.3377965827135128 chr8 146364022 6159546 0.04208374377686888 0.29944079477991126 chr9 141213431 7375606 0.0522302018141603 0.3162249704493856 chr10 135534747 6487969 0.04786941462324787 0.2979174061058886 chr11 135006516 5487120 0.040643371613263465 0.2783240915357521 chr12 133851895 5899574 0.04407538645605279 0.2492763253511545 chr13 115169878 3254725 0.028260210538731317 0.200294362106885 chr14 107349540 2366579 0.022045543930602776 0.17575105873602165 chr15 102531392 2603417 0.025391413782814926 0.20442174626946005 chr16 90354753 3235187 0.03580538812385443 0.22927223685784082 chr17 81195210 3403596 0.04191867968566126 0.2473783014130245 chr18 78077248 5044981 0.06461525129574239 0.4347226457738457 chr19 59128983 3390908 0.05734764624651163 0.3530674576056363 chr20 63025520 2266731 0.03596528834668877 0.22584146123056667 chr21 48129895 1508023 0.03133235590894183 0.21320357404859763 chr22 51304566 1493031 0.029101327940285082 0.20067962678081894 chrMT 16571 405405 24.464727536056966 12.636080642808764 chrX 155270560 7306591 0.047057156231033105 0.2675112342674094 chrY 59373566 280211 0.004719457140236448 0.09116037853164825