BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714159.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 781,834 number of mapped reads = 680,866 (87.09%) number of supplementary alignments = 18,522 (2.37%) number of secondary alignments = 0 number of mapped bases = 90,099,574 bp number of sequenced bases = 88,081,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 631,335 duplication rate = 42.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6022 >>>>>>> ACTG content number of A's = 23,061,785 bp (26.18%) number of C's = 20,266,517 bp (23.01%) number of T's = 22,016,579 bp (25%) number of G's = 22,736,163 bp (25.81%) number of N's = 702 bp (0%) GC percentage = 48.82% >>>>>>> Mismatches and indels general error rate = 0.044 number of mismatches = 3,631,970 number of insertions = 92,142 mapped reads with insertion percentage = 13.06% number of deletions = 323,938 mapped reads with deletion percentage = 45.2% homopolymer indels = 29.02% >>>>>>> Coverage mean coverageData = 0.0291X std coverageData = 12.3288X There is a 0.05% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8154774 0.03271716622924683 10.11997806973689 chr2 243199373 12273185 0.05046552895512605 18.17730827725164 chr3 198022430 2708780 0.01367915745706181 3.6661403021949672 chr4 191154276 2571271 0.013451286854812497 3.4353821989371003 chr5 180915260 3724961 0.02058953456994175 4.69753552435533 chr6 171115067 2733159 0.01597263787413881 4.099050177611629 chr7 159138663 2079244 0.013065611843176035 2.805655344598391 chr8 146364022 3345511 0.02285746834696849 5.310795905919748 chr9 141213431 3102549 0.02197063677321175 4.989874628815778 chr10 135534747 3297393 0.024328764932877323 4.17682864832711 chr11 135006516 3980373 0.029482821406931203 5.317086248885138 chr12 133851895 5512945 0.041186902882473196 11.745542632953205 chr13 115169878 3839453 0.03333730196362629 16.077571220023653 chr14 107349540 7898021 0.07357293752725909 48.76709038983514 chr15 102531392 3656449 0.03566175128101255 9.895433291992791 chr16 90354753 1221574 0.013519753631554944 2.2088694960020736 chr17 81195210 3691874 0.04546911080099429 10.568659434924285 chr18 78077248 2393532 0.03065594729978188 7.231616106296595 chr19 59128983 3409567 0.05766321061195996 8.530684512137146 chr20 63025520 2059261 0.032673447200435635 4.453461041020337 chr21 48129895 785316 0.016316594914657513 3.316929205176607 chr22 51304566 425399 0.008291640163177679 1.3547495152011362 chrMT 16571 143881 8.682698690483374 71.467904595625 chrX 155270560 6587114 0.0424234574796407 5.111801785812132 chrY 59373566 503988 0.008488423956209738 2.280029257521578