BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081199.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 = 7,280,496 number of mapped reads = 6,075,906 (83.45%) number of supplementary alignments = 63,247 (0.87%) number of secondary alignments = 0 number of mapped bases = 402,207,814 bp number of sequenced bases = 402,078,068 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 523,131 duplication rate = 6.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3807 >>>>>>> ACTG content number of A's = 110,338,934 bp (27.44%) number of C's = 78,356,834 bp (19.49%) number of T's = 123,635,723 bp (30.75%) number of G's = 89,516,296 bp (22.26%) number of N's = 230,281 bp (0.06%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 4,136,534 number of insertions = 29,688 mapped reads with insertion percentage = 0.48% number of deletions = 82,930 mapped reads with deletion percentage = 1.35% homopolymer indels = 44.57% >>>>>>> Coverage mean coverageData = 0.1299X std coverageData = 1.0999X There is a 9.24% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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% 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 32790772 0.13155743351187077 2.107122706249215 chr2 243199373 34204810 0.14064514056127933 0.9539493563422496 chr3 198022430 27181248 0.1372634807077158 0.4970466629883955 chr4 191154276 26702867 0.13969275267480807 0.5309477305594664 chr5 180915260 25619195 0.14160881177187595 0.5041249285075778 chr6 171115067 23388344 0.1366819673454004 0.6249291070633869 chr7 159138663 22359691 0.14050445428211245 1.6105024206941712 chr8 146364022 21286623 0.14543617146568985 1.806817580729637 chr9 141213431 17143170 0.1213990048864403 0.8586554795529977 chr10 135534747 19524159 0.14405279407796437 1.280073070397457 chr11 135006516 18645064 0.1381049193210793 1.0031666688376555 chr12 133851895 17389219 0.12991387981470118 0.5088625714331071 chr13 115169878 10870864 0.09438981953249964 0.4020463798915932 chr14 107349540 12229164 0.11391910948104668 1.3662499836302286 chr15 102531392 11267181 0.10989006176761942 0.43118976696414396 chr16 90354753 11226490 0.12424902539438075 0.5624750241844841 chr17 81195210 10302391 0.1268842213721721 0.6247249669398109 chr18 78077248 11021481 0.14116123816249262 1.8696849365933041 chr19 59128983 7465617 0.12625985804626472 1.5379189821129164 chr20 63025520 8266061 0.13115418960446498 0.5024474710712992 chr21 48129895 5257403 0.10923362704198711 0.5203411891211753 chr22 51304566 4198275 0.08183043591090898 0.37823808321671565 chrMT 16571 86966 5.24808400217247 3.6193963172373858 chrX 155270560 22698498 0.14618674654100558 0.6111165642187988 chrY 59373566 1082261 0.018227993919044713 0.3402569584781237