BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063535.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 = 2,715,643 number of mapped reads = 2,352,688 (86.63%) number of supplementary alignments = 20,192 (0.74%) number of secondary alignments = 0 number of mapped bases = 149,991,838 bp number of sequenced bases = 149,916,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,232 duplication rate = 6.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2722 >>>>>>> ACTG content number of A's = 40,370,590 bp (26.93%) number of C's = 26,466,330 bp (17.65%) number of T's = 48,828,470 bp (32.57%) number of G's = 34,247,753 bp (22.84%) number of N's = 2,874 bp (0%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,235,366 number of insertions = 11,306 mapped reads with insertion percentage = 0.48% number of deletions = 46,483 mapped reads with deletion percentage = 1.95% homopolymer indels = 45.11% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.5266X There is a 3.61% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% 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 20023064 0.08033305561954848 1.08541964152027 chr2 243199373 13801633 0.05675028200011026 0.6979601110772835 chr3 198022430 5763063 0.02910308190844845 0.21757416514939412 chr4 191154276 9123667 0.04772933774183529 0.29380781422984115 chr5 180915260 5142994 0.02842764065341973 0.2173558620148771 chr6 171115067 12362736 0.07224808555286368 0.4019017026746875 chr7 159138663 11933021 0.07498505250103804 0.6996843790161116 chr8 146364022 4697403 0.03209397320333272 0.8111555514881537 chr9 141213431 5587433 0.03956729158432529 0.4181814829002339 chr10 135534747 7656605 0.05649182345837854 0.3924020133836486 chr11 135006516 9310280 0.06896170848524082 0.44825711012037056 chr12 133851895 4236650 0.03165177452287844 0.2522830028699361 chr13 115169878 3094454 0.026868605348353326 0.21054331187158656 chr14 107349540 3784239 0.035251562326210246 0.2772899970409124 chr15 102531392 1655154 0.016142899922786575 0.178265291593119 chr16 90354753 3678989 0.04071716072313318 0.2804742795958533 chr17 81195210 4011068 0.04940030329375341 0.30659598964709533 chr18 78077248 4734730 0.06064160970427646 0.6860099221741705 chr19 59128983 3329127 0.0563027948578111 0.6813634284965745 chr20 63025520 2273883 0.036078766188680396 0.26114913386997196 chr21 48129895 3337179 0.06933692666480988 0.35253695474570973 chr22 51304566 1927933 0.03757819528187803 0.24170072111978566 chrMT 16571 22630 1.3656387665198237 1.6629318701045774 chrX 155270560 8143120 0.05244471327983875 0.3327097759235021 chrY 59373566 360783 0.00607649202003464 0.17091522194464406