BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714118.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 = 1,108,404 number of mapped reads = 84,710 (7.64%) number of supplementary alignments = 1,701 (0.15%) number of secondary alignments = 0 number of mapped bases = 8,114,901 bp number of sequenced bases = 8,088,776 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,095 duplication rate = 29.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 21.4192 >>>>>>> ACTG content number of A's = 332,723 bp (4.11%) number of C's = 166,383 bp (2.06%) number of T's = 220,894 bp (2.73%) number of G's = 7,367,737 bp (91.09%) number of N's = 1,039 bp (0.01%) GC percentage = 93.14% >>>>>>> Mismatches and indels general error rate = 0.0324 number of mismatches = 197,748 number of insertions = 9,335 mapped reads with insertion percentage = 7.68% number of deletions = 5,504 mapped reads with deletion percentage = 6.16% homopolymer indels = 58.08% >>>>>>> Coverage mean coverageData = 0.0026X std coverageData = 8.9064X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 95863 3.8460485921918726E-4 0.13811513085405044 chr2 243199373 7356930 0.03025061252933411 31.77346807261725 chr3 198022430 40147 2.0273965934061106E-4 0.05813964114843779 chr4 191154276 37930 1.9842611315689323E-4 0.08005747381086416 chr5 180915260 30813 1.7031730767211125E-4 0.05882740477426546 chr6 171115067 30007 1.7536153026197278E-4 0.04901792940076925 chr7 159138663 24786 1.5575096291967717E-4 0.19872135817376627 chr8 146364022 22585 1.5430704685062563E-4 0.05399633832041132 chr9 141213431 18801 1.3313889384926849E-4 0.058851684530392884 chr10 135534747 22326 1.6472528627658854E-4 0.06410390418089383 chr11 135006516 21758 1.61162591589283E-4 0.06503867790593805 chr12 133851895 46136 3.446794683033811E-4 0.16241234571853022 chr13 115169878 18007 1.563516460441158E-4 0.04937752466198667 chr14 107349540 43160 4.0205109402425014E-4 0.19857725346723212 chr15 102531392 30046 2.9304195928599115E-4 0.1238149863749687 chr16 90354753 21701 2.401755223657133E-4 0.09498498946782263 chr17 81195210 16573 2.0411302587923597E-4 0.1215566366568947 chr18 78077248 26502 3.3943307018198185E-4 0.11839304442739507 chr19 59128983 14952 2.5287091442110544E-4 0.10269355375765954 chr20 63025520 25275 4.0102802801151026E-4 0.2372742139017169 chr21 48129895 13728 2.8522813108152427E-4 0.0972200424736538 chr22 51304566 3633 7.081241073162961E-5 0.025974820433932667 chrMT 16571 2491 0.15032285317723734 1.00587705294654 chrX 155270560 148520 9.565238896542912E-4 0.2205770287056108 chrY 59373566 2231 3.7575644353246356E-5 0.015843060554480343