BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708604.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 4,638,125 number of mapped reads = 4,551,113 (98.12%) number of supplementary alignments = 121 (0%) number of secondary alignments = 0 number of mapped bases = 227,008,643 bp number of sequenced bases = 226,988,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,112 duplication rate = 0.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6729 >>>>>>> ACTG content number of A's = 70,270,500 bp (30.96%) number of C's = 43,086,516 bp (18.98%) number of T's = 69,999,733 bp (30.84%) number of G's = 43,624,003 bp (19.22%) number of N's = 8,125 bp (0%) GC percentage = 38.2% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 332,540 number of insertions = 14,256 mapped reads with insertion percentage = 0.31% number of deletions = 11,506 mapped reads with deletion percentage = 0.25% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.0733X std coverageData = 0.2822X There is a 6.8% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 17500308 0.07021169267217192 0.277574321696629 chr2 243199373 20173680 0.08295120070066957 0.298711048005297 chr3 198022430 18182949 0.09182267382538432 0.3146817642748465 chr4 191154276 17027891 0.08907930994962414 0.3088480257266451 chr5 180915260 15744527 0.08702708107652168 0.3062103279115948 chr6 171115067 14570283 0.08514903599926708 0.3024719865722575 chr7 159138663 13144350 0.08259683569165087 0.2993332982925491 chr8 146364022 12129793 0.08287414375644857 0.29857037674615367 chr9 141213431 9318437 0.0659883194821603 0.26833627060811516 chr10 135534747 9086200 0.06703963523095668 0.26815977985381456 chr11 135006516 10139225 0.07510174545945619 0.2858769653233237 chr12 133851895 11442477 0.08548610387622828 0.3047445354565563 chr13 115169878 8674110 0.07531578699770786 0.28585817195297375 chr14 107349540 6978470 0.06500698559118186 0.2661133607775954 chr15 102531392 5945947 0.057991478356209186 0.25143639490072583 chr16 90354753 4144990 0.04587462045300483 0.2225037938647527 chr17 81195210 3723560 0.0458593554964634 0.22252824402339944 chr18 78077248 6696849 0.08577209329919006 0.30312050237087895 chr19 59128983 1790533 0.030281816279505432 0.17963523361712325 chr20 63025520 3488730 0.0553542438047318 0.2459530752210204 chr21 48129895 2936629 0.06101465627548117 0.260001044103158 chr22 51304566 1287145 0.025088312802412166 0.1644339198894809 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 12571449 0.08096479461399508 0.2954646711854611 chrY 59373566 309961 0.0052205218733198545 0.07598066888936074