BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630581.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 40,626,414 number of mapped reads = 40,071,135 (98.63%) number of supplementary alignments = 69,240 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,140,031 number of mapped paired reads (second in pair) = 19,931,104 number of mapped paired reads (both in pair) = 39,792,436 number of mapped paired reads (singletons) = 278,699 number of mapped bases = 3,918,277,489 bp number of sequenced bases = 3,915,630,264 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,504,801 duplication rate = 7.39% >>>>>>> Insert size mean insert size = 33,341.8605 std insert size = 1,877,982.7196 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.9782 >>>>>>> ACTG content number of A's = 1,097,100,275 bp (28.02%) number of C's = 834,305,680 bp (21.31%) number of T's = 1,104,124,345 bp (28.2%) number of G's = 879,513,655 bp (22.46%) number of N's = 586,309 bp (0.01%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 33,130,812 number of insertions = 635,677 mapped reads with insertion percentage = 1.56% number of deletions = 1,949,822 mapped reads with deletion percentage = 4.74% homopolymer indels = 54.29% >>>>>>> Coverage mean coverageData = 1.2657X std coverageData = 4.5993X There is a 28.33% of reference with a coverageData >= 1X There is a 19.18% of reference with a coverageData >= 2X There is a 13.73% of reference with a coverageData >= 3X There is a 10.39% of reference with a coverageData >= 4X There is a 8.11% of reference with a coverageData >= 5X There is a 6.48% of reference with a coverageData >= 6X There is a 5.28% of reference with a coverageData >= 7X There is a 4.36% of reference with a coverageData >= 8X There is a 3.64% of reference with a coverageData >= 9X There is a 3.08% of reference with a coverageData >= 10X There is a 2.62% of reference with a coverageData >= 11X There is a 2.25% of reference with a coverageData >= 12X There is a 1.94% of reference with a coverageData >= 13X There is a 1.68% of reference with a coverageData >= 14X There is a 1.47% of reference with a coverageData >= 15X There is a 1.29% of reference with a coverageData >= 16X There is a 1.13% of reference with a coverageData >= 17X There is a 1% of reference with a coverageData >= 18X There is a 0.89% of reference with a coverageData >= 19X There is a 0.79% of reference with a coverageData >= 20X There is a 0.71% of reference with a coverageData >= 21X There is a 0.63% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.51% of reference with a coverageData >= 24X There is a 0.46% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.38% of reference with a coverageData >= 27X There is a 0.34% of reference with a coverageData >= 28X There is a 0.31% of reference with a coverageData >= 29X There is a 0.29% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 338109393 1.356503713585532 5.832058782937517 chr2 243199373 328308358 1.3499556102885184 6.648725107092302 chr3 198022430 259297595 1.3094354765770726 3.6932071976987797 chr4 191154276 208927235 1.092977041225068 3.5353554665362847 chr5 180915260 227761834 1.2589420815026882 3.582025539475678 chr6 171115067 217563724 1.2714469147243475 3.7797192803796062 chr7 159138663 196504434 1.2348000812348159 3.7710347115974643 chr8 146364022 194019160 1.3255932526915666 3.9333968835666813 chr9 141213431 170797891 1.2095017434991717 5.602415768002685 chr10 135534747 193717760 1.4292848460476337 4.1479689578077785 chr11 135006516 196417623 1.4548751335824412 5.836935310897097 chr12 133851895 177146837 1.3234540833359139 3.83680924650209 chr13 115169878 108924709 0.9457742848351371 3.057153954453818 chr14 107349540 121664316 1.1333473436402242 3.692389695725436 chr15 102531392 125171687 1.2208132997940768 3.769350941607688 chr16 90354753 126054675 1.395108401214931 5.545008753794685 chr17 81195210 115180047 1.4185571661185432 4.4656987141511815 chr18 78077248 102198447 1.3089401793464852 5.425169185850262 chr19 59128983 72048841 1.2185029632591515 4.663357969582029 chr20 63025520 107515963 1.7059115577309 4.868179522354407 chr21 48129895 51474058 1.0694820339832447 5.2323219885088506 chr22 51304566 64423306 1.2557031668487362 4.212827687621842 chrMT 16571 1164 0.07024319594472271 0.46377669739974364 chrX 155270560 209957146 1.3522018984152566 3.9745297309008407 chrY 59373566 5091286 0.08575004573584144 2.0587024953152486