BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714170.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 = 1,050,514 number of mapped reads = 252,357 (24.02%) number of supplementary alignments = 8,149 (0.78%) number of secondary alignments = 0 number of mapped bases = 32,806,744 bp number of sequenced bases = 32,071,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,477 duplication rate = 42.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.7469 >>>>>>> ACTG content number of A's = 8,480,231 bp (26.44%) number of C's = 7,147,760 bp (22.29%) number of T's = 8,014,547 bp (24.99%) number of G's = 8,428,447 bp (26.28%) number of N's = 216 bp (0%) GC percentage = 48.57% >>>>>>> Mismatches and indels general error rate = 0.0443 number of mismatches = 1,330,378 number of insertions = 33,496 mapped reads with insertion percentage = 12.73% number of deletions = 114,319 mapped reads with deletion percentage = 42.89% homopolymer indels = 29.93% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 3.2243X There is a 0.04% 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 0.01% 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 0.01% 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% 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 2965699 0.011898461829709946 3.1352862515205393 chr2 243199373 4515658 0.01856772056727301 6.166295984135688 chr3 198022430 1021133 0.005156653213476877 0.887987808412158 chr4 191154276 1182627 0.006186767174384318 1.6668075367393849 chr5 180915260 1352489 0.007475814920200761 1.499032426325297 chr6 171115067 1000391 0.005846305749335329 1.065570625591855 chr7 159138663 850683 0.005345545726999102 0.8694301289862792 chr8 146364022 1243070 0.0084930024675053 1.5400320345930467 chr9 141213431 1251077 0.00885947598001496 1.7807892247682182 chr10 135534747 1641706 0.012112805286750563 1.9521836013250913 chr11 135006516 1470978 0.01089560743868096 2.0593532730208297 chr12 133851895 1519115 0.011349222960197912 2.4129637761694025 chr13 115169878 927593 0.008054128528294525 2.8094501215164125 chr14 107349540 2064191 0.019228689754981716 10.645599890024416 chr15 102531392 1202009 0.011723326647120913 2.1549267304376043 chr16 90354753 552109 0.006110458848800129 0.8114558794402182 chr17 81195210 1225572 0.015094141637172931 2.382505818128498 chr18 78077248 830465 0.010636453272533377 2.0956552718829835 chr19 59128983 1010292 0.017086240093119816 1.9192428584414207 chr20 63025520 1059620 0.016812554660397883 3.501746340599873 chr21 48129895 269759 0.005604811728760264 0.9559718390060432 chr22 51304566 244633 0.004768250061797618 0.6322299150259472 chrMT 16571 83403 5.033069820771227 42.77598744673261 chrX 155270560 3089126 0.019895117271426083 2.386880297131294 chrY 59373566 233346 0.003930132813649765 0.6982457588049406