BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081204.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 = 5,557,201 number of mapped reads = 4,616,944 (83.08%) number of supplementary alignments = 54,078 (0.97%) number of secondary alignments = 0 number of mapped bases = 310,479,639 bp number of sequenced bases = 310,381,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 657,683 duplication rate = 9.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7775 >>>>>>> ACTG content number of A's = 85,298,819 bp (27.48%) number of C's = 60,797,768 bp (19.59%) number of T's = 94,950,632 bp (30.59%) number of G's = 69,151,641 bp (22.28%) number of N's = 182,353 bp (0.06%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,168,098 number of insertions = 23,633 mapped reads with insertion percentage = 0.51% number of deletions = 62,074 mapped reads with deletion percentage = 1.33% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.1003X std coverageData = 1.0538X There is a 5.48% of reference with a coverageData >= 1X There is a 2.31% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% 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 25019660 0.1003795292449843 2.1648019533665424 chr2 243199373 26499434 0.10896176940390385 0.9040777461340276 chr3 198022430 20855454 0.10531864496360337 0.5256190872752888 chr4 191154276 20139623 0.10535795181479488 0.5770311391846903 chr5 180915260 18716489 0.10345445154819997 0.5247548444254614 chr6 171115067 18156321 0.10610591643575139 0.6887389042462406 chr7 159138663 16949783 0.10650952245338394 1.4086014461210754 chr8 146364022 15916061 0.10874298739891146 1.8515491236647341 chr9 141213431 12826468 0.09083036867789156 0.8461872453913354 chr10 135534747 15066422 0.11116280019322278 1.0572965458773276 chr11 135006516 14322177 0.10608507962682334 0.8456677696415312 chr12 133851895 13638465 0.10189220705467039 0.5440374913582798 chr13 115169878 9750316 0.08466029633199751 0.4671004022665875 chr14 107349540 9472588 0.08824060168306264 0.6422350735202781 chr15 102531392 8755781 0.0853960999573672 0.46765948159345067 chr16 90354753 8645628 0.09568537030918561 0.5802819089821197 chr17 81195210 8165017 0.10056032862037059 0.6219952385726084 chr18 78077248 8521492 0.10914180786699859 1.6723246197968205 chr19 59128983 6201011 0.10487261382459427 1.4536869676934687 chr20 63025520 6318743 0.10025689593675705 0.5398171461964533 chr21 48129895 4170756 0.0866562455621397 0.5436336326759078 chr22 51304566 3577858 0.06973761360733467 0.4334989465757338 chrMT 16571 327603 19.769657835978517 11.796532968311007 chrX 155270560 17592010 0.11329906970130074 0.6138648080672343 chrY 59373566 874479 0.014728423083093915 0.3665732167305502