BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238063.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 = 2,550,477 number of mapped reads = 2,319,704 (90.95%) number of supplementary alignments = 14,535 (0.57%) number of secondary alignments = 0 number of mapped bases = 155,805,812 bp number of sequenced bases = 155,731,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,353 duplication rate = 2.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8778 >>>>>>> ACTG content number of A's = 42,172,865 bp (27.08%) number of C's = 29,682,960 bp (19.06%) number of T's = 48,331,950 bp (31.04%) number of G's = 35,522,748 bp (22.81%) number of N's = 21,370 bp (0.01%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,138,045 number of insertions = 10,213 mapped reads with insertion percentage = 0.44% number of deletions = 41,755 mapped reads with deletion percentage = 1.78% homopolymer indels = 46.11% >>>>>>> Coverage mean coverageData = 0.0503X std coverageData = 0.407X There is a 4.26% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% 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 13733970 0.05510104626780449 0.8074919179359425 chr2 243199373 17704645 0.07279889245438145 0.44855864038595916 chr3 198022430 10007078 0.05053507322377571 0.2579467572826455 chr4 191154276 7875598 0.041200218822204114 0.24654118236545147 chr5 180915260 8868421 0.049019751014922675 0.25465948489505646 chr6 171115067 9263300 0.054134917295155544 0.32851936131290393 chr7 159138663 9615518 0.0604222620621112 0.6304915765180404 chr8 146364022 9061602 0.06191140333653854 0.44811394551680744 chr9 141213431 4961497 0.03513473870626371 0.30784822296196424 chr10 135534747 7107042 0.052437047748353414 0.4221698340867033 chr11 135006516 6066678 0.044936186635613946 0.28294141234726944 chr12 133851895 7624950 0.056965573778391405 0.2741961579889389 chr13 115169878 6114142 0.053088030535206436 0.26254777186150297 chr14 107349540 3971837 0.03699910591139934 0.23382992382218568 chr15 102531392 6392609 0.062347822216243784 0.2892222024026601 chr16 90354753 3669305 0.040609983184835885 0.2524223999174322 chr17 81195210 2929921 0.036084899589520124 0.2331483707656509 chr18 78077248 4216919 0.05400957523502878 0.571942515412798 chr19 59128983 3659956 0.06189783443425705 0.5236158576773449 chr20 63025520 2078117 0.03297262759593257 0.2105445345657181 chr21 48129895 1735653 0.036061848877916726 0.23512317151667647 chr22 51304566 1923361 0.03748908040660553 0.22121742041264922 chrMT 16571 52257 3.1535212117554763 2.764249686393641 chrX 155270560 6814709 0.0438892537001219 0.26072476321575494 chrY 59373566 356727 0.006008178791214932 0.16666318264015192