BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818943.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,318,763 number of mapped reads = 2,164,553 (93.35%) number of supplementary alignments = 26,237 (1.13%) number of secondary alignments = 0 number of mapped bases = 200,566,756 bp number of sequenced bases = 200,452,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 936,581 duplication rate = 36.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3906 >>>>>>> ACTG content number of A's = 58,479,491 bp (29.17%) number of C's = 41,887,397 bp (20.9%) number of T's = 57,497,252 bp (28.68%) number of G's = 42,578,261 bp (21.24%) number of N's = 9,744 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,282,458 number of insertions = 26,032 mapped reads with insertion percentage = 1.17% number of deletions = 61,660 mapped reads with deletion percentage = 2.79% homopolymer indels = 41.89% >>>>>>> Coverage mean coverageData = 0.0648X std coverageData = 0.7137X There is a 3.02% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.78% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 24315553 0.09755463357501525 1.2642451957592125 chr2 243199373 17685694 0.07272096873374752 1.0036419398349814 chr3 198022430 13944832 0.07042046701477202 0.4950212502973859 chr4 191154276 12183867 0.06373839630979534 0.5067697624567364 chr5 180915260 10391450 0.05743821720732679 0.45685825907832306 chr6 171115067 10650984 0.06224457136787376 0.49317251773161785 chr7 159138663 10138953 0.06371143761588596 0.6058091503197751 chr8 146364022 13616957 0.09303486481124439 0.631781582552049 chr9 141213431 7624010 0.05398926961841186 0.766190529745075 chr10 135534747 9776641 0.07213383443287794 0.9056090962068811 chr11 135006516 7675200 0.05685058934488762 0.49598750535727043 chr12 133851895 9533274 0.07122255534746072 0.5062519200516012 chr13 115169878 3155828 0.027401505105354024 0.3002861631531452 chr14 107349540 3980864 0.03708319569883579 0.39858135614369494 chr15 102531392 5871702 0.05726735866416405 0.4450227509959265 chr16 90354753 6417412 0.07102462003299373 0.8252335997461204 chr17 81195210 4278332 0.052691926038494145 0.47747522830359856 chr18 78077248 5306098 0.06795959304303348 0.969536041315307 chr19 59128983 3245765 0.054892961713885725 1.097074641150495 chr20 63025520 4322082 0.06857669718552103 0.5205769911372958 chr21 48129895 2647843 0.055014518523258775 0.46520778893122017 chr22 51304566 1340617 0.02613055921767275 0.33468725875038696 chrMT 16571 12340 0.7446744312352905 1.5762778171554936 chrX 155270560 11855026 0.07635076475540502 0.5613178269455269 chrY 59373566 595432 0.010028570626867855 0.6179569159247822