BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080947.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 = 2,845,841 number of mapped reads = 2,527,078 (88.8%) number of supplementary alignments = 30,247 (1.06%) number of secondary alignments = 0 number of mapped bases = 175,028,364 bp number of sequenced bases = 174,966,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,191 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.142 >>>>>>> ACTG content number of A's = 51,199,451 bp (29.26%) number of C's = 30,988,432 bp (17.71%) number of T's = 56,083,820 bp (32.05%) number of G's = 35,835,975 bp (20.48%) number of N's = 858,553 bp (0.49%) GC percentage = 38.19% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 1,963,727 number of insertions = 13,386 mapped reads with insertion percentage = 0.53% number of deletions = 37,924 mapped reads with deletion percentage = 1.49% homopolymer indels = 50.47% >>>>>>> Coverage mean coverageData = 0.0565X std coverageData = 0.3967X There is a 4.26% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.07% 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% 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 13373173 0.05365351928250562 0.5884250808804642 chr2 243199373 15277494 0.06281880504683703 0.38352827190105115 chr3 198022430 12332448 0.06227803587704686 0.31494230867287365 chr4 191154276 12810315 0.06701558169695351 0.33583873594675173 chr5 180915260 11612858 0.06418948849312103 0.3213497619308356 chr6 171115067 10814472 0.06319999863016154 0.36067203798633485 chr7 159138663 9603003 0.06034361995362497 0.43389252881134854 chr8 146364022 9322580 0.06369447814162964 0.7565613999942702 chr9 141213431 7395789 0.05237312731251463 0.36788218458323696 chr10 135534747 7791017 0.057483539626926816 0.3433244953930179 chr11 135006516 8156259 0.06041381735974877 0.3448220480808192 chr12 133851895 7886490 0.05891952444901882 0.3087313812333724 chr13 115169878 5963770 0.05178237663844708 0.2890598846299112 chr14 107349540 5473946 0.05099179744971427 0.2957474263728881 chr15 102531392 4651188 0.04536355070649972 0.26849905211748726 chr16 90354753 4120778 0.0456066544722888 0.2796276025567303 chr17 81195210 3481893 0.04288298533866715 0.2804323099322356 chr18 78077248 4795966 0.06142590988862722 0.5505801187879872 chr19 59128983 2395539 0.04051378661459474 0.42112994801705483 chr20 63025520 2985127 0.047363782163161845 0.28053026958461613 chr21 48129895 2286795 0.04751298543244277 0.28913652633526216 chr22 51304566 1561291 0.030431813807761283 0.21703173996732184 chrMT 16571 30340 1.8309094200712088 1.8692854779516666 chrX 155270560 10538487 0.06787176525929964 0.34621411179162637 chrY 59373566 367346 0.006187029426529644 0.11894793116316704