BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818772.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,440,836 number of mapped reads = 1,398,506 (97.06%) number of supplementary alignments = 9,717 (0.67%) number of secondary alignments = 0 number of mapped bases = 95,121,201 bp number of sequenced bases = 95,082,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 611,769 duplication rate = 37.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8039 >>>>>>> ACTG content number of A's = 27,045,172 bp (28.44%) number of C's = 19,828,233 bp (20.85%) number of T's = 26,210,791 bp (27.57%) number of G's = 21,992,406 bp (23.13%) number of N's = 5,724 bp (0.01%) GC percentage = 43.98% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 473,241 number of insertions = 8,494 mapped reads with insertion percentage = 0.6% number of deletions = 24,408 mapped reads with deletion percentage = 1.73% homopolymer indels = 44.23% >>>>>>> Coverage mean coverageData = 0.0307X std coverageData = 0.4027X There is a 1.49% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 7851167 0.03149908701731981 0.5845803312364315 chr2 243199373 8401686 0.03454649531518324 0.5929894201870622 chr3 198022430 6484943 0.03274852752791691 0.3258563937292341 chr4 191154276 6298889 0.03295186030784893 0.3522262042875737 chr5 180915260 5928198 0.03276781626934069 0.32733527044792426 chr6 171115067 5605430 0.032758249161074754 0.34584800858945897 chr7 159138663 5279432 0.033175043075484426 0.3714168526284135 chr8 146364022 4958570 0.03387833930936935 0.37021139417021603 chr9 141213431 4101446 0.029044305282831064 0.3400743475360031 chr10 135534747 4565441 0.033684653574481534 0.41294258409223256 chr11 135006516 4411075 0.032673052610290305 0.3532307111167064 chr12 133851895 4294479 0.0320838117383396 0.33385495388483716 chr13 115169878 3083983 0.026777687478317897 0.28831039519043006 chr14 107349540 2961605 0.027588427486508093 0.3209114888665318 chr15 102531392 2760319 0.026921696332768016 0.29405425537296065 chr16 90354753 2795276 0.030936679114157945 0.4282787745604595 chr17 81195210 2429891 0.029926531380360985 0.3228225809306582 chr18 78077248 2630245 0.03368772680102659 0.4575945289139559 chr19 59128983 1827813 0.030912302347564476 0.4619021620148148 chr20 63025520 2050057 0.03252741111854373 0.3392629682850685 chr21 48129895 1275636 0.026504026239824542 0.30713224481845736 chr22 51304566 1156220 0.02253639568844613 0.29470978953311855 chrMT 16571 139912 8.443183875445055 7.985432743156936 chrX 155270560 2914220 0.018768657754567254 0.2649149231747152 chrY 59373566 915268 0.015415412306547327 0.5889756743163318