BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081959.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,258,173 number of mapped reads = 2,983,572 (91.57%) number of supplementary alignments = 17,295 (0.53%) number of secondary alignments = 0 number of mapped bases = 207,922,221 bp number of sequenced bases = 207,838,069 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 130,404 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7922 >>>>>>> ACTG content number of A's = 60,411,194 bp (29.07%) number of C's = 38,765,411 bp (18.65%) number of T's = 65,505,749 bp (31.52%) number of G's = 43,128,491 bp (20.75%) number of N's = 27,224 bp (0.01%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,600,060 number of insertions = 15,208 mapped reads with insertion percentage = 0.5% number of deletions = 47,100 mapped reads with deletion percentage = 1.56% homopolymer indels = 48.05% >>>>>>> Coverage mean coverageData = 0.0672X std coverageData = 0.5608X There is a 5.59% of reference with a coverageData >= 1X There is a 0.82% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% 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% 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 19477836 0.07814558664630168 0.952862521272044 chr2 243199373 17833627 0.07332924744012395 0.7663633184828258 chr3 198022430 12540728 0.06332983591808261 0.2919284260403106 chr4 191154276 10427759 0.05455153407083606 0.29401632698414104 chr5 180915260 10099892 0.05582664502706958 0.2735427177238268 chr6 171115067 19193069 0.11216469324703009 0.5179275446736079 chr7 159138663 13286686 0.08349125064598538 0.7919234399902794 chr8 146364022 11013048 0.07524422907700637 0.9034101733782346 chr9 141213431 10069577 0.0713075019046878 0.5615269142244049 chr10 135534747 8970399 0.0661852344033962 0.6002263328958608 chr11 135006516 9678499 0.07168912499008566 0.39792413277979716 chr12 133851895 9169729 0.0685065310431354 0.31470449753051605 chr13 115169878 5862048 0.05089914222189243 0.25787046186446977 chr14 107349540 4763981 0.044378215314196966 0.26740890274833073 chr15 102531392 4921698 0.048001864638685485 0.24902368543668743 chr16 90354753 4466186 0.049429452814729075 0.31285209104509615 chr17 81195210 5887129 0.07250586580168954 0.37540095863891654 chr18 78077248 6550568 0.08389855134238337 0.8505711219646328 chr19 59128983 3772500 0.06380119881310997 0.7160607242134814 chr20 63025520 5054377 0.080195720717576 0.3336444670530317 chr21 48129895 2065451 0.0429140973609022 0.2689931192216455 chr22 51304566 1504595 0.029326726981766107 0.19319019348206054 chrMT 16571 7603 0.45881359000663813 0.6617492210588503 chrX 155270560 10872114 0.07002044688960998 0.36147296028669623 chrY 59373566 433122 0.00729486249823701 0.18125858552389848