BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234032.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 = 2,303,936 number of mapped reads = 2,009,818 (87.23%) number of supplementary alignments = 10,257 (0.45%) number of secondary alignments = 0 number of mapped bases = 132,699,259 bp number of sequenced bases = 132,631,563 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,304 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6059 >>>>>>> ACTG content number of A's = 36,507,637 bp (27.53%) number of C's = 24,499,492 bp (18.47%) number of T's = 41,579,221 bp (31.35%) number of G's = 30,021,422 bp (22.64%) number of N's = 23,791 bp (0.02%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,017,535 number of insertions = 9,634 mapped reads with insertion percentage = 0.47% number of deletions = 38,210 mapped reads with deletion percentage = 1.88% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.0429X std coverageData = 0.4085X There is a 3.69% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.06% 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 11039460 0.04429060178750768 0.8381159830754329 chr2 243199373 7053987 0.029004955534979934 0.4210072857419322 chr3 198022430 13402806 0.0676832720414551 0.293344731410364 chr4 191154276 5188673 0.027143902342001494 0.2119064794597075 chr5 180915260 6595931 0.03645867684130128 0.21696054170529477 chr6 171115067 9466842 0.05532442096405222 0.36478143340821084 chr7 159138663 8042400 0.05053705899238327 0.5774968948990928 chr8 146364022 7786190 0.053197431264904706 0.4393095505558644 chr9 141213431 6339206 0.0448909565833012 0.3524115986292957 chr10 135534747 6509759 0.04803018520409383 0.4042570999671654 chr11 135006516 5448861 0.040359985291376604 0.3126999207707067 chr12 133851895 4847242 0.036213473107721036 0.2184218789448205 chr13 115169878 5674846 0.04927369984710759 0.24797533789857784 chr14 107349540 7079963 0.06595242979150166 0.3093302485750864 chr15 102531392 2602370 0.025381202276079505 0.17930967170335177 chr16 90354753 3701490 0.04096619023461887 0.2708846832101803 chr17 81195210 2837634 0.03494829313207023 0.226318187035608 chr18 78077248 3196546 0.040940812872912735 0.6839787043139867 chr19 59128983 4173438 0.07058193441277351 0.49744023486976613 chr20 63025520 3725496 0.059110912531939445 0.28336685274734175 chr21 48129895 2387756 0.0496106629777605 0.2697954081665708 chr22 51304566 1228269 0.023940734631689508 0.17161536408239528 chrMT 16571 20847 1.2580411562367992 1.3602874745685885 chrX 155270560 4026714 0.025933531765455087 0.2069609348374993 chrY 59373566 322533 0.005432265934641689 0.1326266234861413