BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,806,250 number of mapped reads = 8,505,300 (86.73%) number of secondary alignments = 0 number of mapped bases = 337,937,647 bp number of sequenced bases = 337,901,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 303,211 duplication rate = 2.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.972 >>>>>>> ACTG content number of A's = 99,824,605 bp (29.54%) number of C's = 69,220,636 bp (20.49%) number of T's = 99,820,455 bp (29.54%) number of G's = 69,029,735 bp (20.43%) number of N's = 6,297 bp (0%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,040,782 number of insertions = 8,082 mapped reads with insertion percentage = 0.09% number of deletions = 27,831 mapped reads with deletion percentage = 0.33% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.1092X std coverageData = 0.9533X There is a 9.03% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 27647417 0.11092215894619577 2.075243233565292 chr2 243199373 29129368 0.11977567063875613 0.5821919101303062 chr3 198022430 23740430 0.11988758041197656 0.40039981259379087 chr4 191154276 23138786 0.12104770285128227 0.43914725041525643 chr5 180915260 21584881 0.11930934405422737 0.4044584386388888 chr6 171115067 20356018 0.11896099131936758 0.4804574546992709 chr7 159138663 18815957 0.11823623904644719 0.7915640463853153 chr8 146364022 17934852 0.12253593304507579 2.4511256959477485 chr9 141213431 14353906 0.10164688938122324 0.5393223141904983 chr10 135534747 16099760 0.1187869557907538 0.6701594084953839 chr11 135006516 15610892 0.11563065593071079 0.5625309985682767 chr12 133851895 15616234 0.11666800832367745 0.4132799672896398 chr13 115169878 11383700 0.09884268523754101 0.3557781079396432 chr14 107349540 10551988 0.0982956051791186 0.4077390352497027 chr15 102531392 9769040 0.09527852699005589 0.3509299757072037 chr16 90354753 9192713 0.10174022610631231 0.42569420875742625 chr17 81195210 8543315 0.10521944582691516 0.4087160973331095 chr18 78077248 9243641 0.11839096839068917 1.120435984323688 chr19 59128983 6200180 0.10485855980306646 1.5228669387761775 chr20 63025520 6914468 0.10970901945751499 0.3957085302327408 chr21 48129895 4412567 0.09168037869187123 0.4184094728073088 chr22 51304566 3698962 0.07209810526415913 0.3446747745237233 chrMT 16571 9273 0.5595920584153038 0.9759692177416014 chrX 155270560 11062189 0.0712446003930172 0.38713750083109033 chrY 59373566 2927110 0.049299885406916606 0.49250994407869114