BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080644.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 = 1,441,335 number of mapped reads = 1,301,148 (90.27%) number of supplementary alignments = 11,634 (0.81%) number of secondary alignments = 0 number of mapped bases = 85,603,843 bp number of sequenced bases = 85,571,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,273 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.042 >>>>>>> ACTG content number of A's = 22,939,913 bp (26.81%) number of C's = 15,974,947 bp (18.67%) number of T's = 26,844,302 bp (31.37%) number of G's = 19,809,152 bp (23.15%) number of N's = 3,565 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 591,765 number of insertions = 6,414 mapped reads with insertion percentage = 0.49% number of deletions = 20,106 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.29% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2371X There is a 2.41% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% 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 9998100 0.04011263827503162 0.26706210713786427 chr2 243199373 5566061 0.022886822985353668 0.3686069567718286 chr3 198022430 5249325 0.02650873943926453 0.1811792740842147 chr4 191154276 3444843 0.01802127094452232 0.1564617050585979 chr5 180915260 3833697 0.021190567340753898 0.16192405570710044 chr6 171115067 4991071 0.029167922424972664 0.22878638695561632 chr7 159138663 5251718 0.033000893063931294 0.44005066570695883 chr8 146364022 11696307 0.07991244596981627 0.3493365292591651 chr9 141213431 2797866 0.01981303039085567 0.1773247535848455 chr10 135534747 4044140 0.029838400037740874 0.20386033560225164 chr11 135006516 3492970 0.02587260306754379 0.18975892343938647 chr12 133851895 2714758 0.02028180475143815 0.15800691689331622 chr13 115169878 1754779 0.01523644055609749 0.1381468996502839 chr14 107349540 1659725 0.015460941891320634 0.14056685729580673 chr15 102531392 1599476 0.015599866234138322 0.15257594685086176 chr16 90354753 2114867 0.023406261760241878 0.1741125923909529 chr17 81195210 1473531 0.018148004050977884 0.15397113483568428 chr18 78077248 2707267 0.034674211365646496 0.23905531712809377 chr19 59128983 1369485 0.023160976741304684 0.19064276357298485 chr20 63025520 2189288 0.03473653212222604 0.21124851507490763 chr21 48129895 1256311 0.026102508638342136 0.18271004045151312 chr22 51304566 820518 0.0159930794463791 0.13942404691128865 chrMT 16571 17129 1.0336732846539134 1.2519832157559507 chrX 155270560 5397855 0.03476418839476073 0.21361393723350464 chrY 59373566 162756 0.0027412198889990875 0.06134229068634753