BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084833.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 = 1,762,351 number of mapped reads = 1,596,472 (90.59%) number of supplementary alignments = 21,109 (1.2%) number of secondary alignments = 0 number of mapped bases = 106,208,714 bp number of sequenced bases = 106,171,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,135 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9868 >>>>>>> ACTG content number of A's = 29,644,307 bp (27.92%) number of C's = 20,817,178 bp (19.61%) number of T's = 31,405,889 bp (29.58%) number of G's = 24,289,169 bp (22.88%) number of N's = 14,583 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 872,083 number of insertions = 9,448 mapped reads with insertion percentage = 0.58% number of deletions = 22,125 mapped reads with deletion percentage = 1.37% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 0.0343X std coverageData = 0.3997X There is a 3.11% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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% 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 8919959 0.035787108430113 0.7751627137410043 chr2 243199373 9234964 0.03797281171444467 0.5701735637429876 chr3 198022430 7884987 0.039818655896708265 0.21314654973287778 chr4 191154276 5704033 0.029839944569170926 0.19364218539768835 chr5 180915260 5489747 0.030344300419986682 0.19590070975567708 chr6 171115067 5807622 0.03393986340197617 0.21273295014969099 chr7 159138663 6147836 0.038631944519981296 0.45696378594239206 chr8 146364022 5788527 0.0395488380334342 0.3842237219428723 chr9 141213431 7098962 0.05027115303217865 0.45037298494983746 chr10 135534747 3694093 0.027255689642450138 0.26457230599491377 chr11 135006516 4460034 0.03303569436604082 0.37286767539682386 chr12 133851895 4454539 0.03327961102082268 0.20143018614243932 chr13 115169878 2817156 0.024460875090967796 0.16394289474347068 chr14 107349540 2193883 0.020436817894142815 0.20291793729161448 chr15 102531392 2695516 0.026289665510441915 0.18109765386563936 chr16 90354753 2341320 0.02591252725797391 0.22171497626942974 chr17 81195210 3325890 0.04096165278715333 0.25390721787890325 chr18 78077248 4056881 0.051959835981923955 0.891718636388918 chr19 59128983 2728949 0.04615247652745862 0.5086313140691177 chr20 63025520 2265705 0.03594900922673863 0.21802523932219503 chr21 48129895 981003 0.02038240474033862 0.17736543270741215 chr22 51304566 1146218 0.022341442280205626 0.1567938787114523 chrMT 16571 46778 2.8228833504314768 2.328961691212481 chrX 155270560 6619307 0.04263079234080176 0.2746003501984088 chrY 59373566 304805 0.005133681881260088 0.17238139363849816