BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240269.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,895,509 number of mapped reads = 1,468,840 (77.49%) number of supplementary alignments = 5,603 (0.3%) number of secondary alignments = 0 number of mapped bases = 88,904,125 bp number of sequenced bases = 88,854,844 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 152,502 duplication rate = 8.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0833 >>>>>>> ACTG content number of A's = 23,716,531 bp (26.69%) number of C's = 14,958,645 bp (16.83%) number of T's = 29,542,285 bp (33.25%) number of G's = 20,617,809 bp (23.2%) number of N's = 19,574 bp (0.02%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 857,300 number of insertions = 6,278 mapped reads with insertion percentage = 0.42% number of deletions = 29,135 mapped reads with deletion percentage = 1.96% homopolymer indels = 50.59% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2795X There is a 2.14% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 6596341 0.026464692338720393 0.32062449418965977 chr2 243199373 10619497 0.04366580747722569 0.3695159295313969 chr3 198022430 6207171 0.03134579754424789 0.23478598848540302 chr4 191154276 6440921 0.03369488318430292 0.2501891506874564 chr5 180915260 4299792 0.02376688400967392 0.20322478193858268 chr6 171115067 4465703 0.026097660938297153 0.23716710137297536 chr7 159138663 5058771 0.03178844728637691 0.5074247491386052 chr8 146364022 5607358 0.038311040673643146 0.34018644802098263 chr9 141213431 3092614 0.021900282275557768 0.2474964844376819 chr10 135534747 3666559 0.02705253878549683 0.24079316920649857 chr11 135006516 4070767 0.03015237427503129 0.27078670788022885 chr12 133851895 4546108 0.03396371788385962 0.23913434949524465 chr13 115169878 1883971 0.016358192200220965 0.16798419220249058 chr14 107349540 3251444 0.03028838316400797 0.23007105140696005 chr15 102531392 2460367 0.023996231320062445 0.213918529839684 chr16 90354753 2259770 0.02500997374205649 0.20375810080216655 chr17 81195210 2040899 0.025135706896995524 0.2193915781705499 chr18 78077248 1944745 0.024907960383029892 0.326474348618392 chr19 59128983 1348376 0.0228039775350102 0.2547278385581825 chr20 63025520 1682049 0.026688379564341554 0.21728972583283218 chr21 48129895 1476215 0.030671477675153873 0.2342839621195381 chr22 51304566 690813 0.013464941892306428 0.1454173808372324 chrMT 16571 64857 3.913885703940619 4.866586392026367 chrX 155270560 4945987 0.03185399086600834 0.2513548348231127 chrY 59373566 183030 0.003082684978025406 0.07084489824387513