BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082933.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 = 2,005,638 number of mapped reads = 1,776,735 (88.59%) number of supplementary alignments = 18,143 (0.9%) number of secondary alignments = 0 number of mapped bases = 118,283,603 bp number of sequenced bases = 118,238,784 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,413 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2655 >>>>>>> ACTG content number of A's = 31,752,658 bp (26.85%) number of C's = 22,335,660 bp (18.89%) number of T's = 36,963,833 bp (31.26%) number of G's = 27,181,494 bp (22.99%) number of N's = 5,139 bp (0%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 887,266 number of insertions = 9,382 mapped reads with insertion percentage = 0.52% number of deletions = 27,323 mapped reads with deletion percentage = 1.52% homopolymer indels = 48.53% >>>>>>> Coverage mean coverageData = 0.0382X std coverageData = 0.281X There is a 3.22% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 9356775 0.0375396256284553 0.362115782156598 chr2 243199373 12683831 0.05215404482148891 0.425308040408483 chr3 198022430 8461743 0.042731235042414134 0.238453085175837 chr4 191154276 7146766 0.03738742417668962 0.22702894446846114 chr5 180915260 6113279 0.03379084218766289 0.21260264677220037 chr6 171115067 7292233 0.042615960872691594 0.2946827012020412 chr7 159138663 5626778 0.03535770562556505 0.2615478095985823 chr8 146364022 9337982 0.06379970892027004 0.32844957913476275 chr9 141213431 3519487 0.0249231746235243 0.23435706737160816 chr10 135534747 4132517 0.030490461608343136 0.22276182161371821 chr11 135006516 5481854 0.04060436608852272 0.276020856444837 chr12 133851895 4809638 0.03593253573287102 0.2185476581872165 chr13 115169878 2459950 0.021359317581286317 0.1688777152964892 chr14 107349540 2838039 0.02643736526490938 0.19867163304428478 chr15 102531392 2094837 0.02043117682436224 0.16758171461739105 chr16 90354753 5676456 0.06282409958001878 0.30057450847723566 chr17 81195210 3053469 0.03760651644351927 0.23977744248290273 chr18 78077248 4075941 0.05220395319261253 0.4945157035739823 chr19 59128983 2282409 0.03860051169829862 0.3220251888246393 chr20 63025520 2616018 0.04150728149486113 0.2400829999432484 chr21 48129895 2812178 0.058428924476149384 0.28453780386228095 chr22 51304566 2077351 0.04049056764265387 0.23353083912629424 chrMT 16571 20664 1.246997767183634 1.3713404482750984 chrX 155270560 4099834 0.026404451687428707 0.19969989704061694 chrY 59373566 213574 0.0035971226656657273 0.07620061318871611