BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084969.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 = 2,552,002 number of mapped reads = 2,379,634 (93.25%) number of supplementary alignments = 24,204 (0.95%) number of secondary alignments = 0 number of mapped bases = 166,683,456 bp number of sequenced bases = 166,620,109 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,119 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2795 >>>>>>> ACTG content number of A's = 49,607,731 bp (29.77%) number of C's = 30,664,212 bp (18.4%) number of T's = 52,658,351 bp (31.6%) number of G's = 33,665,026 bp (20.2%) number of N's = 24,789 bp (0.01%) GC percentage = 38.61% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,401,153 number of insertions = 13,880 mapped reads with insertion percentage = 0.58% number of deletions = 38,872 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.69% >>>>>>> Coverage mean coverageData = 0.0538X std coverageData = 0.662X There is a 4.67% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 13111678 0.05260439451422671 1.3524439011090292 chr2 243199373 13943430 0.05733333037828185 0.5691623983381745 chr3 198022430 12972539 0.06551045252802927 0.28862480327441065 chr4 191154276 12418664 0.06496670783341514 0.28657105208924566 chr5 180915260 9443541 0.052198697887618765 0.25833216272638104 chr6 171115067 10468784 0.061179790789550985 0.4496931059782183 chr7 159138663 8968150 0.056354312842253805 0.5394380059749214 chr8 146364022 9310715 0.063613413137827 1.555192558822243 chr9 141213431 7204282 0.05101697444062527 0.5421018673300568 chr10 135534747 8352561 0.061626713332781004 0.5841304626136651 chr11 135006516 6991055 0.051783093195294366 0.5253358840870389 chr12 133851895 7961014 0.059476289073083353 0.2848360088750741 chr13 115169878 6084650 0.052831956633660755 0.25083044782046177 chr14 107349540 5807277 0.05409689692196166 0.29446607728399204 chr15 102531392 4347667 0.04240327684227675 0.22581710578849443 chr16 90354753 3995884 0.04422439182585115 0.3209044118197568 chr17 81195210 3140057 0.03867293403145333 0.2791161232760286 chr18 78077248 4099360 0.05250389972761335 1.1150225391401103 chr19 59128983 2168447 0.036673165848294734 0.8564145260489041 chr20 63025520 2762231 0.04382718302046536 0.2507786054289123 chr21 48129895 2142821 0.04452162216435336 0.2742776542391555 chr22 51304566 1251016 0.024384106475045516 0.17001273078515294 chrMT 16571 28909 1.7445537384587533 1.5237928629996425 chrX 155270560 9371179 0.06035386875657562 0.3426002453700928 chrY 59373566 337545 0.005685105725332381 0.14253429753551788