BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240208.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 = 1,965,064 number of mapped reads = 1,484,271 (75.53%) number of supplementary alignments = 7,197 (0.37%) number of secondary alignments = 0 number of mapped bases = 89,360,528 bp number of sequenced bases = 89,314,579 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,052 duplication rate = 9.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0133 >>>>>>> ACTG content number of A's = 23,330,437 bp (26.12%) number of C's = 15,074,530 bp (16.88%) number of T's = 29,820,715 bp (33.39%) number of G's = 21,067,241 bp (23.59%) number of N's = 21,656 bp (0.02%) GC percentage = 40.47% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 842,267 number of insertions = 6,031 mapped reads with insertion percentage = 0.4% number of deletions = 27,409 mapped reads with deletion percentage = 1.83% homopolymer indels = 49.99% >>>>>>> Coverage mean coverageData = 0.0289X std coverageData = 0.2809X There is a 2.12% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.05% 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 6562798 0.026330116946829994 0.3662694446665527 chr2 243199373 9752062 0.040099042525080855 0.38025348302115886 chr3 198022430 6355442 0.03209455615709796 0.23679029240563296 chr4 191154276 6004961 0.031414212256491714 0.23907479722138122 chr5 180915260 4903469 0.027103678263514088 0.21785109918488146 chr6 171115067 4896745 0.028616679324912984 0.2515459124878268 chr7 159138663 5341187 0.03356310087888573 0.4496835439939256 chr8 146364022 5019783 0.034296563673277575 0.32878431706182243 chr9 141213431 3248500 0.0230041857704031 0.2525265164567644 chr10 135534747 3903950 0.028804052734904946 0.2500701148969525 chr11 135006516 4043894 0.029953324623235224 0.24926458306018182 chr12 133851895 4168666 0.031143869871995463 0.23367461589670857 chr13 115169878 2106181 0.018287602944235124 0.17761632178278014 chr14 107349540 3090126 0.02878564733486515 0.22710828462392302 chr15 102531392 2404408 0.023450457007352443 0.21647961886338596 chr16 90354753 2474998 0.02739200670494888 0.22025173735761683 chr17 81195210 2331453 0.02871416922254404 0.22739489373886218 chr18 78077248 2029169 0.025989248494004295 0.3248055850912936 chr19 59128983 1566226 0.026488295934330545 0.2906815056843569 chr20 63025520 1839305 0.029183495828356512 0.22675484963553644 chr21 48129895 1348099 0.02800959777701572 0.22490978790642804 chr22 51304566 814418 0.015874181646912285 0.16076394645846503 chrMT 16571 48067 2.9006698449097823 3.814797997851505 chrX 155270560 4906713 0.0316010517383334 0.2456785029424925 chrY 59373566 199908 0.0033669528961760525 0.07603466429209843