BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004069.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 = 1,209,142 number of mapped reads = 1,092,368 (90.34%) number of supplementary alignments = 8,274 (0.68%) number of secondary alignments = 0 number of mapped bases = 75,007,697 bp number of sequenced bases = 74,975,392 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,753 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2972 >>>>>>> ACTG content number of A's = 21,683,100 bp (28.92%) number of C's = 13,766,544 bp (18.36%) number of T's = 24,021,462 bp (32.04%) number of G's = 15,490,925 bp (20.66%) number of N's = 13,361 bp (0.02%) GC percentage = 39.02% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 650,680 number of insertions = 5,679 mapped reads with insertion percentage = 0.52% number of deletions = 18,516 mapped reads with deletion percentage = 1.68% homopolymer indels = 46.5% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.247X There is a 2.09% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5237627 0.02101349629134926 0.4166983912797731 chr2 243199373 5903655 0.024274959787828072 0.23447363760970247 chr3 198022430 5659112 0.02857813632526376 0.19015577330754607 chr4 191154276 5032486 0.026326829330252596 0.19165056718350873 chr5 180915260 5206644 0.028779462826961085 0.1923739622260447 chr6 171115067 4477653 0.026167496986107014 0.1934212367575136 chr7 159138663 4314315 0.027110413765383964 0.31056530476976063 chr8 146364022 4988221 0.0340809232476544 0.4336639608477512 chr9 141213431 2856145 0.020225731927722937 0.21416051677615536 chr10 135534747 3518082 0.025957048490303374 0.23324746264996055 chr11 135006516 2874790 0.021293712964195 0.18814543151727786 chr12 133851895 3273740 0.024457927921005526 0.17822316228258483 chr13 115169878 2600530 0.022579949246798715 0.17092286628013725 chr14 107349540 2102204 0.01958279467243176 0.16565742574177317 chr15 102531392 2438055 0.02377861991769311 0.1734295053786863 chr16 90354753 1884805 0.020860053704092357 0.17244781333907155 chr17 81195210 1447277 0.01782465985370319 0.15393975161271095 chr18 78077248 2136874 0.027368715659650298 0.35687859760747537 chr19 59128983 1029951 0.01741871663850535 0.25663309654662486 chr20 63025520 1592682 0.025270430136871542 0.18240561621396736 chr21 48129895 971822 0.02019165011683487 0.16814262612908776 chr22 51304566 575049 0.011208534538621768 0.11739800467223314 chrMT 16571 4294 0.25912739122563516 0.5316796132356497 chrX 155270560 4694759 0.030235989359476773 0.20614959723546117 chrY 59373566 186925 0.0031482865624072503 0.08698007228515454