BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084790.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 = 2,377,270 number of mapped reads = 2,131,110 (89.65%) number of supplementary alignments = 21,832 (0.92%) number of secondary alignments = 0 number of mapped bases = 143,900,806 bp number of sequenced bases = 143,843,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,363 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8461 >>>>>>> ACTG content number of A's = 39,758,990 bp (27.64%) number of C's = 27,379,073 bp (19.03%) number of T's = 44,741,373 bp (31.1%) number of G's = 31,922,671 bp (22.19%) number of N's = 41,316 bp (0.03%) GC percentage = 41.23% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,239,066 number of insertions = 11,250 mapped reads with insertion percentage = 0.52% number of deletions = 35,332 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.05% >>>>>>> Coverage mean coverageData = 0.0465X std coverageData = 0.377X There is a 3.91% of reference with a coverageData >= 1X There is a 0.55% 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 12115645 0.04860828410935032 0.6051258111837874 chr2 243199373 10853087 0.0446262951508514 0.441506784112991 chr3 198022430 8989613 0.045396943164468795 0.24448405668060053 chr4 191154276 8879737 0.046453248056036164 0.26681614363213596 chr5 180915260 8554821 0.04728634278833085 0.2508595503153268 chr6 171115067 7721741 0.04512601453149652 0.2966084118842671 chr7 159138663 7859305 0.04938652148912424 0.4478995302239113 chr8 146364022 7024216 0.047991411441262524 0.4092652744403513 chr9 141213431 6294511 0.04457444986235056 0.38576114474291623 chr10 135534747 7341648 0.05416801346152216 0.3613149220546792 chr11 135006516 6515742 0.048262426089122984 0.3739710072689363 chr12 133851895 5864695 0.04381480740336175 0.2452750616447311 chr13 115169878 4312459 0.037444330712931725 0.22481248330576012 chr14 107349540 5096458 0.047475359465909216 0.2729216465144358 chr15 102531392 4256871 0.04151773341768344 0.2424013922286896 chr16 90354753 4842316 0.05359226647434917 0.29936606892231316 chr17 81195210 4190340 0.051608216790128385 0.30231048380457276 chr18 78077248 3789829 0.04853947977264773 0.8302816304183219 chr19 59128983 2907304 0.049168848380159016 0.4651500045567426 chr20 63025520 3600567 0.057128715479063084 0.28818838411888054 chr21 48129895 2024919 0.0420719596417154 0.25300500901869083 chr22 51304566 1871687 0.03648187960502385 0.21726675763071854 chrMT 16571 6232 0.37607869169030234 0.684570588207776 chrX 155270560 8606767 0.05543077193770667 0.29128694098728763 chrY 59373566 380296 0.006405139957401245 0.14388116858660333