BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083784.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 = 3,821,499 number of mapped reads = 2,830,842 (74.08%) number of supplementary alignments = 15,731 (0.41%) number of secondary alignments = 0 number of mapped bases = 180,887,341 bp number of sequenced bases = 180,821,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,895 duplication rate = 3.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8872 >>>>>>> ACTG content number of A's = 50,927,888 bp (28.16%) number of C's = 34,753,595 bp (19.22%) number of T's = 54,575,438 bp (30.18%) number of G's = 40,562,414 bp (22.43%) number of N's = 2,028 bp (0%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,575,432 number of insertions = 14,119 mapped reads with insertion percentage = 0.49% number of deletions = 41,130 mapped reads with deletion percentage = 1.44% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.0584X std coverageData = 0.4548X There is a 4.99% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 14199775 0.05696986809112103 0.7527211194642803 chr2 243199373 15316803 0.06298043786486242 0.5922633001439869 chr3 198022430 12212033 0.0616699481972825 0.281978396043979 chr4 191154276 11697972 0.06119649659314971 0.2980600540450859 chr5 180915260 11140043 0.061576027362202614 0.28184942241779487 chr6 171115067 10760072 0.0628820839020564 0.37186212586658063 chr7 159138663 10137122 0.06369993192666197 0.6454317388755295 chr8 146364022 9217847 0.06297891294624303 0.42895890260196423 chr9 141213431 7532751 0.05334302089154678 0.4127403064487524 chr10 135534747 8510513 0.06279211190027897 0.462955301130447 chr11 135006516 8131237 0.06022847815730613 0.39453242844157355 chr12 133851895 8200547 0.061265826681049226 0.28637848578632047 chr13 115169878 5834916 0.05066355978947898 0.25491118968160675 chr14 107349540 5545314 0.05165661632085242 0.28847186098734945 chr15 102531392 5091204 0.04965507539388522 0.26248565754807374 chr16 90354753 5115270 0.05661318115716613 0.32607161946198315 chr17 81195210 4820300 0.05936680254906663 0.33062263766191574 chr18 78077248 4935108 0.0632080167579677 0.956859187535563 chr19 59128983 3543794 0.05993328178839132 0.5464103938998138 chr20 63025520 3660546 0.058080377599423215 0.28883643866594516 chr21 48129895 2404027 0.049948727293088836 0.2779469087411792 chr22 51304566 1984296 0.03867679145750887 0.22161509919154876 chrMT 16571 37437 2.259187737613904 1.9738795125690953 chrX 155270560 10396261 0.06695577706424193 0.3594209884108239 chrY 59373566 462153 0.007783817465166232 0.1611227272512785