BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094069.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 361,632 number of mapped reads = 341,950 (94.56%) number of supplementary alignments = 12,441 (3.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,717 number of mapped paired reads (second in pair) = 170,233 number of mapped paired reads (both in pair) = 339,590 number of mapped paired reads (singletons) = 2,360 number of mapped bases = 44,866,755 bp number of sequenced bases = 43,757,802 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,929 duplication rate = 49.36% >>>>>>> Insert size mean insert size = 415,204.7735 std insert size = 5,814,391.0002 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 38.1712 >>>>>>> ACTG content number of A's = 11,685,558 bp (26.71%) number of C's = 10,151,005 bp (23.2%) number of T's = 11,172,839 bp (25.53%) number of G's = 10,747,899 bp (24.56%) number of N's = 501 bp (0%) GC percentage = 47.76% >>>>>>> Mismatches and indels general error rate = 0.0438 number of mismatches = 1,862,325 number of insertions = 28,897 mapped reads with insertion percentage = 8.25% number of deletions = 146,802 mapped reads with deletion percentage = 40.75% homopolymer indels = 26.49% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 3.7634X 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 0.01% 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% 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 277156 0.0011119571092262194 0.46589512820571255 chr2 243199373 1561825 0.006421994352756822 2.342610991059698 chr3 198022430 904008 0.004565179813216109 1.5830670647696197 chr4 191154276 543084 0.0028410769110914368 1.1072976129402394 chr5 180915260 433816 0.002397896119984572 1.1790272356931777 chr6 171115067 856396 0.005004795983278317 2.628022667703962 chr7 159138663 1893027 0.011895456228635025 4.281107886244355 chr8 146364022 671540 0.00458814940190698 1.463143627555613 chr9 141213431 610823 0.004325530480170828 1.9909217718890186 chr10 135534747 942776 0.006955972699753518 2.496734621624117 chr11 135006516 1234723 0.00914565486602143 2.785250867343308 chr12 133851895 1338772 0.010001890522356819 2.821230623522816 chr13 115169878 999997 0.008682799855010699 2.5271859009693873 chr14 107349540 289354 0.0026954377261420963 1.1112229351648608 chr15 102531392 856192 0.008350535219496484 2.822243278056541 chr16 90354753 428970 0.004747619640994426 1.8586312520701098 chr17 81195210 890428 0.010966508984951205 3.6507936832601207 chr18 78077248 133060 0.0017042096565698626 0.5851044132508325 chr19 59128983 203063 0.0034342379945888806 0.8225320395674861 chr20 63025520 221190 0.0035095307424674958 0.9202350330248564 chr21 48129895 505721 0.01050741955701337 3.8605463080146847 chr22 51304566 70664 0.0013773432953316474 0.39125926778561065 chrMT 16571 927153 55.95033492245489 260.8231959525877 chrX 155270560 27680155 0.17827046543787825 13.507428614833277 chrY 59373566 392862 0.006616782963650861 1.3540628471752147