BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238319.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 = 2,736,146 number of mapped reads = 2,517,266 (92%) number of supplementary alignments = 22,292 (0.81%) number of secondary alignments = 0 number of mapped bases = 167,961,405 bp number of sequenced bases = 167,879,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,060 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6271 >>>>>>> ACTG content number of A's = 47,220,319 bp (28.13%) number of C's = 31,517,141 bp (18.77%) number of T's = 52,155,321 bp (31.07%) number of G's = 36,944,162 bp (22.01%) number of N's = 42,963 bp (0.03%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,370,477 number of insertions = 12,569 mapped reads with insertion percentage = 0.5% number of deletions = 47,247 mapped reads with deletion percentage = 1.86% homopolymer indels = 46.13% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.5119X There is a 4.61% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% 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 18200176 0.07301958136345024 1.063014221952274 chr2 243199373 12008656 0.04937782467062528 0.5779126272459851 chr3 198022430 9938911 0.050190834442340695 0.2534957061794049 chr4 191154276 9179785 0.04802291213197867 0.2724065592273352 chr5 180915260 13743477 0.0759663778500498 0.31677162056008945 chr6 171115067 11700460 0.06837773087509588 0.3914130620334014 chr7 159138663 8342682 0.0524239794574622 0.6436263323004705 chr8 146364022 6773744 0.0462801165712705 0.6435557738218253 chr9 141213431 6148823 0.04354276329423651 0.47353278181615865 chr10 135534747 7087920 0.052295962156479324 0.4475633967343295 chr11 135006516 6534316 0.04840000463385041 0.39078202724060496 chr12 133851895 8815941 0.06586340073855511 0.30102384421523704 chr13 115169878 2416018 0.020977863673694263 0.16336808514052512 chr14 107349540 4655963 0.04337198836622868 0.2877520954138859 chr15 102531392 4176754 0.040736343460547185 0.2338196091503975 chr16 90354753 4432578 0.04905749673179893 0.29294240391083437 chr17 81195210 3854402 0.04747080523592463 0.292309810473406 chr18 78077248 5239156 0.06710221138941783 0.8638515386185822 chr19 59128983 2838643 0.04800764119349051 0.7207245417781546 chr20 63025520 4967251 0.07881332831526024 0.3273719040272444 chr21 48129895 1703836 0.035400783650161714 0.2514184289212355 chr22 51304566 2077056 0.040484817667105884 0.2262508361787402 chrMT 16571 9354 0.5644801158650655 0.9938632495900054 chrX 155270560 12638151 0.08139438023537753 0.3812281037131473 chrY 59373566 477352 0.008039806805607735 0.1757058708297249