BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082937.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 = 1,915,034 number of mapped reads = 1,755,715 (91.68%) number of supplementary alignments = 18,993 (0.99%) number of secondary alignments = 0 number of mapped bases = 117,509,169 bp number of sequenced bases = 117,464,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,167 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7546 >>>>>>> ACTG content number of A's = 32,712,537 bp (27.85%) number of C's = 21,298,723 bp (18.13%) number of T's = 37,863,352 bp (32.23%) number of G's = 25,583,575 bp (21.78%) number of N's = 5,841 bp (0%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 839,571 number of insertions = 10,103 mapped reads with insertion percentage = 0.57% number of deletions = 27,527 mapped reads with deletion percentage = 1.55% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.038X std coverageData = 0.3124X There is a 3.13% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.09% 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% 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 11848875 0.04753799590332816 0.42263742714709085 chr2 243199373 11697322 0.04809766512021394 0.485863756461125 chr3 198022430 8732819 0.04410015067485032 0.24509924449754117 chr4 191154276 7108140 0.03718535702544263 0.23508454942075716 chr5 180915260 6161776 0.03405890691586768 0.21735677722231964 chr6 171115067 7792680 0.045540583518574665 0.31577634746250377 chr7 159138663 5320508 0.033433157597911954 0.24646741306759348 chr8 146364022 9548043 0.06523490451772362 0.4399636760444742 chr9 141213431 5089907 0.03604407147362633 0.327090009017682 chr10 135534747 4300452 0.031729516564486596 0.25152665920168993 chr11 135006516 4672776 0.03461148497454745 0.26351107261272066 chr12 133851895 3123214 0.02333335661777519 0.18573696816014107 chr13 115169878 2827712 0.02455253100120502 0.18451415128378368 chr14 107349540 2334570 0.02174736845635296 0.19982014699038944 chr15 102531392 2300330 0.022435372768566334 0.18117033082549333 chr16 90354753 4149589 0.04592551982295829 0.26790945307481995 chr17 81195210 2773928 0.03416369019798089 0.24439573021288125 chr18 78077248 5033312 0.06446579674529512 0.6240180817802425 chr19 59128983 1600633 0.027070193309429995 0.29351862179708793 chr20 63025520 2281514 0.03619984412663315 0.2354211959828173 chr21 48129895 2926500 0.060804204954114274 0.30077827459375445 chr22 51304566 1098984 0.021420783483481764 0.1696645928713461 chrMT 16571 60497 3.6507754510892525 3.0301162711625738 chrX 155270560 4519053 0.029104377545878628 0.21974058541410155 chrY 59373566 206035 0.0034701469674231797 0.08713827212873652