BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472836.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,684,848 number of mapped reads = 2,313,578 (86.17%) number of supplementary alignments = 25,023 (0.93%) number of secondary alignments = 0 number of mapped bases = 149,623,974 bp number of sequenced bases = 149,564,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,862 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7484 >>>>>>> ACTG content number of A's = 40,541,968 bp (27.11%) number of C's = 30,336,380 bp (20.28%) number of T's = 43,808,483 bp (29.29%) number of G's = 34,874,350 bp (23.32%) number of N's = 2,912 bp (0%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,270,098 number of insertions = 11,809 mapped reads with insertion percentage = 0.51% number of deletions = 33,655 mapped reads with deletion percentage = 1.44% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0483X std coverageData = 0.3514X There is a 4.22% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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% 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 11005679 0.04415507153340252 0.4475986943859879 chr2 243199373 14437871 0.05936639894215517 0.5298345871805872 chr3 198022430 10749065 0.0542820578456693 0.25750147855506345 chr4 191154276 8257711 0.04319919581605384 0.259161534689252 chr5 180915260 7601086 0.042014620546658145 0.227486298054683 chr6 171115067 9159494 0.05352827287850695 0.2769044154979586 chr7 159138663 9204491 0.0578394390557372 0.45390688987711464 chr8 146364022 8351014 0.057056467059917224 0.353084619643937 chr9 141213431 8666889 0.0613743957541829 0.4170901060356293 chr10 135534747 6208831 0.04580988371933878 0.34532801483446596 chr11 135006516 4958979 0.036731404875302465 0.339818681561947 chr12 133851895 6255556 0.04673490801157503 0.24862386295634833 chr13 115169878 6039918 0.05244355646534591 0.26083181561389496 chr14 107349540 2997559 0.027923352070255727 0.22043159863106482 chr15 102531392 2784993 0.027162344582232923 0.19869149159684993 chr16 90354753 5118655 0.05665064459863003 0.2966563032150511 chr17 81195210 3327197 0.040977749795831554 0.24528075133941668 chr18 78077248 2502180 0.032047492247677584 0.6341070436234337 chr19 59128983 3637440 0.06151703979079092 0.3880458469439652 chr20 63025520 6545019 0.10384712414907485 0.3771286771543071 chr21 48129895 1779607 0.036975085858799404 0.2593414768716884 chr22 51304566 1772017 0.03453916752750623 0.22055700223090124 chrMT 16571 29216 1.7630800796572326 1.7247538300189735 chrX 155270560 7447861 0.047966987431487335 0.27913570966016293 chrY 59373566 785646 0.013232252211362882 0.19253978278226894