BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714072.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 = 543,670 number of mapped reads = 101,184 (18.61%) number of supplementary alignments = 3,178 (0.58%) number of secondary alignments = 0 number of mapped bases = 11,286,845 bp number of sequenced bases = 11,096,813 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,969 duplication rate = 39.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.195 >>>>>>> ACTG content number of A's = 2,193,990 bp (19.77%) number of C's = 1,505,362 bp (13.57%) number of T's = 2,049,238 bp (18.47%) number of G's = 5,347,970 bp (48.19%) number of N's = 253 bp (0%) GC percentage = 61.76% >>>>>>> Mismatches and indels general error rate = 0.0415 number of mismatches = 411,855 number of insertions = 12,943 mapped reads with insertion percentage = 11.25% number of deletions = 30,350 mapped reads with deletion percentage = 27.42% homopolymer indels = 32.8% >>>>>>> Coverage mean coverageData = 0.0036X std coverageData = 4.6734X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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% 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 721743 0.0028956517624884872 0.4342032007754125 chr2 243199373 4233945 0.017409358205870046 16.609996095542197 chr3 198022430 406179 0.002051176727808057 0.5212482129494898 chr4 191154276 423995 0.002218077507196334 0.40533273567733136 chr5 180915260 628983 0.0034766718960025813 0.5440562783918697 chr6 171115067 305138 0.0017832327997159946 0.32188891857130614 chr7 159138663 369248 0.002320290952802588 0.39662913221645624 chr8 146364022 495723 0.0033869184053988348 0.5267984059222667 chr9 141213431 359677 0.002547045259455526 0.44651465628321296 chr10 135534747 297557 0.0021954296339963654 0.3729909541631159 chr11 135006516 363466 0.00269221079669962 0.37061569711249803 chr12 133851895 490853 0.003667135231817226 0.5056404107581325 chr13 115169878 182730 0.0015866127773444371 0.32493359214022355 chr14 107349540 101503 9.455373539560579E-4 0.23289560688289399 chr15 102531392 195751 0.0019091811413230399 0.31587204319155504 chr16 90354753 186413 0.002063123342277301 0.38264389996747217 chr17 81195210 182671 0.002249775571736313 0.394738392891967 chr18 78077248 304124 0.003895168026414046 0.4893889197601496 chr19 59128983 138190 0.0023370941455225095 0.49767266604038685 chr20 63025520 173171 0.002747633022305885 0.41387466179127574 chr21 48129895 39072 8.118031423089537E-4 0.14650668113935064 chr22 51304566 119152 0.002322444360995082 0.3593409268164903 chrMT 16571 34340 2.072294973145857 16.436625878343868 chrX 155270560 513709 0.003308476507072558 0.47157064117943365 chrY 59373566 19512 3.2863109485456877E-4 0.08538714846404814