BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708524.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,305,801 number of mapped reads = 2,084,609 (63.06%) number of supplementary alignments = 597 (0.02%) number of secondary alignments = 0 number of mapped bases = 98,472,662 bp number of sequenced bases = 98,449,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,248 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.1252 >>>>>>> ACTG content number of A's = 27,775,620 bp (28.21%) number of C's = 18,215,877 bp (18.5%) number of T's = 31,526,066 bp (32.02%) number of G's = 20,931,068 bp (21.26%) number of N's = 1,227 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 521,218 number of insertions = 5,497 mapped reads with insertion percentage = 0.26% number of deletions = 15,012 mapped reads with deletion percentage = 0.72% homopolymer indels = 47.61% >>>>>>> Coverage mean coverageData = 0.0318X std coverageData = 0.3232X There is a 2.72% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.06% 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 0.01% 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 7840814 0.03145755051097746 0.4671062118412337 chr2 243199373 8670439 0.035651568065514706 0.49032639716313814 chr3 198022430 6884916 0.03476836437165224 0.2251456975529475 chr4 191154276 6805809 0.03560374971679943 0.23109404490590824 chr5 180915260 6111756 0.03378242388176653 0.21567443261424035 chr6 171115067 5931874 0.034665994666618107 0.32753631588563326 chr7 159138663 5723199 0.035963598613367766 0.42702467257519444 chr8 146364022 5255708 0.03590846936414469 0.47712207096893117 chr9 141213431 4180208 0.029602056761867078 0.27116053944489815 chr10 135534747 4646575 0.03428327497449787 0.2776020309091105 chr11 135006516 4496503 0.033305822068617784 0.29014496512715726 chr12 133851895 4535271 0.033882755264690124 0.22147422737250175 chr13 115169878 3327501 0.02889211187668359 0.2674128275731332 chr14 107349540 3111822 0.028987753464057693 0.2092450150420593 chr15 102531392 2785857 0.027170771269739515 0.20469521767977847 chr16 90354753 2655608 0.029390905423647164 0.21479513943559042 chr17 81195210 2455090 0.03023688220031699 0.24554735966365912 chr18 78077248 2567362 0.03288233212318139 0.39898562377190366 chr19 59128983 1784080 0.030172681982370643 0.3536477803180506 chr20 63025520 1917024 0.03041663123128536 0.209700324593608 chr21 48129895 1330199 0.027637687553650387 0.22582099133778122 chr22 51304566 991412 0.019324050027048276 0.18086638037757755 chrMT 16571 102108 6.1618490133365516 4.223736866681723 chrX 155270560 3574592 0.02302169838248796 0.21213292552012888 chrY 59373566 786935 0.013253962209377823 0.15562186580722084