BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083651.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 = 1,858,633 number of mapped reads = 1,482,273 (79.75%) number of supplementary alignments = 9,534 (0.51%) number of secondary alignments = 0 number of mapped bases = 90,688,582 bp number of sequenced bases = 90,659,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,157 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1255 >>>>>>> ACTG content number of A's = 27,024,785 bp (29.81%) number of C's = 17,415,140 bp (19.21%) number of T's = 26,604,698 bp (29.35%) number of G's = 19,609,592 bp (21.63%) number of N's = 5,336 bp (0.01%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 761,115 number of insertions = 6,249 mapped reads with insertion percentage = 0.42% number of deletions = 18,340 mapped reads with deletion percentage = 1.23% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.257X There is a 2.67% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8025776 0.032199622884791126 0.5204037407456304 chr2 243199373 10580961 0.043507353121342136 0.26547820050935234 chr3 198022430 7948613 0.04013996293248194 0.2161903200636625 chr4 191154276 4298638 0.02248779409988192 0.16161863175321534 chr5 180915260 4850345 0.02681003802553748 0.17498888105716165 chr6 171115067 6672749 0.038995683530311215 0.2554888526580084 chr7 159138663 4885305 0.03069841676375024 0.25665796620959663 chr8 146364022 5846695 0.03994625810433113 0.34125707626345236 chr9 141213431 4076105 0.02886485351382759 0.2043158982424693 chr10 135534747 4584900 0.03382822561361331 0.26203626506196065 chr11 135006516 2870788 0.021264069950520017 0.17092804004972287 chr12 133851895 3241233 0.024215069947272693 0.16670533202191629 chr13 115169878 2827293 0.02454889289715146 0.1665092522465234 chr14 107349540 1912630 0.017816843928721075 0.1435965329491513 chr15 102531392 2289738 0.022332067821726247 0.16013769234187364 chr16 90354753 2656298 0.029398541989263144 0.18882764586364487 chr17 81195210 1819243 0.02240579216434073 0.16288606779357137 chr18 78077248 2353550 0.030143864701788668 0.30077316482021976 chr19 59128983 2030255 0.03433603787841235 0.36957140434264935 chr20 63025520 1468097 0.023293691190489185 0.16428778838034472 chr21 48129895 1425495 0.029617662785260596 0.18617707338326325 chr22 51304566 649418 0.012658093628547603 0.11929960374710066 chrMT 16571 136634 8.24536841470038 4.668677471354955 chrX 155270560 3064213 0.019734668310592812 0.15702263517413279 chrY 59373566 173610 0.0029240285146423578 0.06901387972358769