BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089589.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 11,105,952 number of mapped reads = 9,449,083 (85.08%) number of supplementary alignments = 391 (0%) number of secondary alignments = 0 number of mapped bases = 444,666,675 bp number of sequenced bases = 444,577,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,545,945 duplication rate = 19.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4939 >>>>>>> ACTG content number of A's = 140,713,385 bp (31.65%) number of C's = 84,264,695 bp (18.95%) number of T's = 121,362,426 bp (27.3%) number of G's = 98,218,776 bp (22.09%) number of N's = 18,693 bp (0%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,273,353 number of insertions = 18,771 mapped reads with insertion percentage = 0.2% number of deletions = 58,559 mapped reads with deletion percentage = 0.62% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.1436X std coverageData = 1.1044X There is a 5.54% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 1.53% of reference with a coverageData >= 3X There is a 1.01% of reference with a coverageData >= 4X There is a 0.71% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.31% of reference with a coverageData >= 8X There is a 0.25% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 34612878 0.13886777036354905 1.0535617417122003 chr2 243199373 43931988 0.18064186374362076 1.433192246156235 chr3 198022430 45886261 0.23172254274427398 1.452859557309166 chr4 191154276 17406973 0.09106243064110164 0.7793514513953501 chr5 180915260 20339961 0.11242811137103637 0.8729733560273589 chr6 171115067 29440747 0.17205233598745573 1.1637625550491664 chr7 159138663 27076836 0.17014618251505606 1.268608638917321 chr8 146364022 32921163 0.22492660798840305 1.5663732356004862 chr9 141213431 15464722 0.10951310998172688 0.9349149279087821 chr10 135534747 17370793 0.12816486830495208 0.9645424291888871 chr11 135006516 22716547 0.16826259704383453 1.1488086970196785 chr12 133851895 14999312 0.11205901866387473 0.8635045602277159 chr13 115169878 13316010 0.11562059655911071 0.9048440587347092 chr14 107349540 15923499 0.14833318335597898 1.089410487275526 chr15 102531392 10433133 0.10175549942792154 0.815069141611986 chr16 90354753 9072828 0.1004134004992521 0.8149516666740237 chr17 81195210 10090456 0.12427403045081108 0.9165980011788739 chr18 78077248 22504057 0.2882281019945785 1.6453757374298126 chr19 59128983 7078624 0.11971496279582552 1.0628157566363678 chr20 63025520 9985212 0.15843125134072675 1.07579598414616 chr21 48129895 7471730 0.15524093705170144 1.1633416600458868 chr22 51304566 3513867 0.0684903367080427 0.6165801302964289 chrMT 16571 54128 3.2664293042061434 9.088831946217274 chrX 155270560 12208204 0.07862536207765336 0.7364256409855101 chrY 59373566 846746 0.01426132969678796 0.3004467626176529