BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080772.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 = 5,690,357 number of mapped reads = 4,046,825 (71.12%) number of supplementary alignments = 29,942 (0.53%) number of secondary alignments = 0 number of mapped bases = 255,245,503 bp number of sequenced bases = 255,156,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 388,236 duplication rate = 7.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5922 >>>>>>> ACTG content number of A's = 77,020,152 bp (30.19%) number of C's = 53,037,129 bp (20.79%) number of T's = 65,475,153 bp (25.66%) number of G's = 59,537,148 bp (23.33%) number of N's = 87,212 bp (0.03%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,976,936 number of insertions = 19,052 mapped reads with insertion percentage = 0.47% number of deletions = 46,951 mapped reads with deletion percentage = 1.15% homopolymer indels = 42.14% >>>>>>> Coverage mean coverageData = 0.0825X std coverageData = 0.5462X There is a 5.55% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 29865439 0.11982092112821657 0.8019208748851985 chr2 243199373 18184535 0.07477212944952781 0.520302072257462 chr3 198022430 15366126 0.07759790645938443 0.4001351221799259 chr4 191154276 13373358 0.06996107165293022 0.46331634458213933 chr5 180915260 18040613 0.09971858095331483 0.46084248710065717 chr6 171115067 15030072 0.087836052450016 0.5876678552019622 chr7 159138663 16974131 0.1066625210996023 0.6533838564502575 chr8 146364022 11139425 0.0761076721436365 0.5347703219222768 chr9 141213431 9237255 0.06541343082302135 0.41285058110271067 chr10 135534747 12670322 0.09348393884558621 0.8590606577923924 chr11 135006516 11100277 0.08222030557399171 0.48565155012446637 chr12 133851895 8828133 0.06595448648672475 0.37049519793564994 chr13 115169878 10160656 0.08822320711323493 0.43174483363406446 chr14 107349540 7045758 0.06563379777873292 0.41998379177028977 chr15 102531392 7008936 0.06835892757605398 0.3748750701529951 chr16 90354753 8773675 0.09710252874024236 0.5354901784896547 chr17 81195210 6905466 0.08504770170555627 0.44866786841574685 chr18 78077248 3509658 0.04495109766163889 0.5904120259677533 chr19 59128983 5427199 0.09178576604302496 0.8315472078991247 chr20 63025520 4913036 0.07795312121185197 0.4300086080727203 chr21 48129895 4630496 0.09620831294146809 0.5579290001717622 chr22 51304566 1869961 0.0364482373752075 0.2805341455883694 chrMT 16571 24417 1.473477762355923 1.925947110926815 chrX 155270560 14272028 0.09191715415980982 0.44918468277561013 chrY 59373566 894531 0.015066149134448148 0.4945174156862893