BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081022.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 = 2,120,044 number of mapped reads = 1,502,140 (70.85%) number of supplementary alignments = 7,036 (0.33%) number of secondary alignments = 0 number of mapped bases = 91,497,238 bp number of sequenced bases = 91,464,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,494 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6324 >>>>>>> ACTG content number of A's = 25,969,559 bp (28.39%) number of C's = 18,714,039 bp (20.46%) number of T's = 25,805,510 bp (28.21%) number of G's = 20,974,103 bp (22.93%) number of N's = 1,044 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 697,264 number of insertions = 6,309 mapped reads with insertion percentage = 0.42% number of deletions = 18,696 mapped reads with deletion percentage = 1.23% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2343X There is a 2.61% of reference with a coverageData >= 1X There is a 0.26% 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% 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 7103742 0.028500398400211006 0.2696761278494978 chr2 243199373 7643008 0.03142692312779935 0.2636782235677311 chr3 198022430 6304163 0.031835600643826054 0.1974838261531761 chr4 191154276 5253627 0.027483701175484036 0.1932758826042126 chr5 180915260 5361909 0.029637682304964212 0.19160041494678212 chr6 171115067 5222856 0.030522478771550843 0.23357833490378266 chr7 159138663 5438444 0.03417424714696767 0.37814007011310113 chr8 146364022 4646005 0.031742807668950226 0.23498121978924744 chr9 141213431 3705417 0.026239834084903723 0.21635722883442102 chr10 135534747 4503283 0.03322604055180035 0.2279054527578152 chr11 135006516 4492143 0.03327352733108082 0.23891593165220706 chr12 133851895 3773747 0.028193452173389102 0.1875420723439993 chr13 115169878 2981346 0.025886508276061558 0.17772772543602147 chr14 107349540 2832267 0.026383596986069992 0.18819813709841007 chr15 102531392 2716972 0.026498928250188975 0.19630607370030775 chr16 90354753 2609368 0.02887914485251263 0.20043074031837285 chr17 81195210 2786605 0.034319820097761924 0.21812225811289124 chr18 78077248 2493489 0.031936179410421844 0.3779367262303949 chr19 59128983 1871139 0.03164503945552387 0.24087147674729353 chr20 63025520 1870979 0.02968605415710969 0.1986801645090455 chr21 48129895 1166116 0.024228517431837324 0.18282168225459525 chr22 51304566 1163118 0.02267084765905631 0.1673126122779217 chrMT 16571 26891 1.6227747269325932 1.7298262566088942 chrX 155270560 5294814 0.03410056613436572 0.22080324303680204 chrY 59373566 235790 0.003971295913066768 0.08781692747434755