BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3212161.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 = 2,000,938 number of mapped reads = 1,795,124 (89.71%) number of supplementary alignments = 19,176 (0.96%) number of secondary alignments = 0 number of mapped bases = 116,895,667 bp number of sequenced bases = 116,850,286 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,700 duplication rate = 3.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4234 >>>>>>> ACTG content number of A's = 33,826,380 bp (28.95%) number of C's = 22,259,664 bp (19.05%) number of T's = 36,025,159 bp (30.83%) number of G's = 24,731,547 bp (21.17%) number of N's = 7,536 bp (0.01%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,045,230 number of insertions = 8,632 mapped reads with insertion percentage = 0.48% number of deletions = 27,543 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.3127X There is a 3.19% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% 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 13877049 0.0556750829519498 0.5941851017768034 chr2 243199373 7688988 0.03161598611522736 0.30984556853869144 chr3 198022430 7501159 0.037880350220932044 0.22560501315330714 chr4 191154276 5210787 0.027259589003386982 0.1955852473332761 chr5 180915260 7324559 0.04048613146287383 0.23176914764950068 chr6 171115067 7715678 0.04509058223376671 0.2580624569038685 chr7 159138663 7748168 0.04868815568721977 0.3921178899415678 chr8 146364022 6665786 0.04554251727244828 0.4113663398938194 chr9 141213431 3256436 0.02306038439077371 0.22450800585273858 chr10 135534747 3538530 0.02610791755120921 0.28405989430264805 chr11 135006516 6515950 0.048263966755500896 0.33418595496086656 chr12 133851895 3678172 0.027479416709042484 0.19124436386120422 chr13 115169878 1883246 0.016351897151440933 0.14819513741336232 chr14 107349540 4453859 0.04148931611630567 0.23967970980626138 chr15 102531392 2340059 0.022822854097211517 0.18048434611214725 chr16 90354753 4012030 0.04440308746126504 0.24859123210811818 chr17 81195210 2211757 0.02723999359075492 0.21252764797153129 chr18 78077248 2966539 0.03799492266940556 0.3775023692240409 chr19 59128983 3143545 0.05316419868070452 0.4296276267543708 chr20 63025520 3011700 0.047785405023235035 0.25391899825689956 chr21 48129895 2217712 0.04607764051843454 0.2528862996733958 chr22 51304566 882367 0.017198605675759933 0.14764853182355844 chrMT 16571 17970 1.0844245971878583 1.1780876647360647 chrX 155270560 8742280 0.056303525922750584 0.28809743756987216 chrY 59373566 291341 0.004906914299201769 0.09186577539413737