BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081026.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 = 2,088,393 number of mapped reads = 1,432,255 (68.58%) number of supplementary alignments = 6,686 (0.32%) number of secondary alignments = 0 number of mapped bases = 90,840,034 bp number of sequenced bases = 90,809,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,293 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9431 >>>>>>> ACTG content number of A's = 25,147,915 bp (27.69%) number of C's = 17,737,010 bp (19.53%) number of T's = 27,196,224 bp (29.95%) number of G's = 20,727,238 bp (22.82%) number of N's = 1,196 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 620,102 number of insertions = 5,815 mapped reads with insertion percentage = 0.4% number of deletions = 17,413 mapped reads with deletion percentage = 1.2% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0293X std coverageData = 0.2262X There is a 2.56% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 6994429 0.02806183178977917 0.2734974506386209 chr2 243199373 7372118 0.030313063348234866 0.2453822564156971 chr3 198022430 6279589 0.031711503590780094 0.19867772781916884 chr4 191154276 5658537 0.029601937860913977 0.1981716327095263 chr5 180915260 5427789 0.03000183069134135 0.19303828767825032 chr6 171115067 5204887 0.030417467562923607 0.23385028939001617 chr7 159138663 4712759 0.029614167362961945 0.2737706642664411 chr8 146364022 4880464 0.03334469723713933 0.23022609391774593 chr9 141213431 3511101 0.024863789337432076 0.21889548237741055 chr10 135534747 4347533 0.03207688874056776 0.23392757792317304 chr11 135006516 4808558 0.035617229023227295 0.24825289896047326 chr12 133851895 4320204 0.03227600177046429 0.20212057287154725 chr13 115169878 2813960 0.02443312477938025 0.174742515564166 chr14 107349540 2752886 0.02564413410621042 0.1858587524363889 chr15 102531392 2683743 0.02617484214005404 0.1841338032068211 chr16 90354753 2748611 0.030420214861303422 0.20718543613438295 chr17 81195210 2062002 0.025395611391361633 0.18795581316639753 chr18 78077248 2474494 0.03169289470858399 0.3719323741478265 chr19 59128983 1591678 0.026918744738092314 0.24575757338457474 chr20 63025520 1912637 0.03034702450689816 0.1975691665662479 chr21 48129895 1166540 0.024237326925396367 0.183975331551016 chr22 51304566 1095221 0.021347437185220513 0.16417163567577675 chrMT 16571 25072 1.5130046466718967 1.545676751962282 chrX 155270560 5754726 0.03706257000683195 0.22758110060364423 chrY 59373566 240496 0.004050556774710146 0.09182972254906563