BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238642.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 = 3,070,518 number of mapped reads = 2,742,190 (89.31%) number of supplementary alignments = 25,368 (0.83%) number of secondary alignments = 0 number of mapped bases = 167,896,563 bp number of sequenced bases = 167,812,067 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 675,107 duplication rate = 18.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3292 >>>>>>> ACTG content number of A's = 41,075,555 bp (24.48%) number of C's = 29,647,502 bp (17.67%) number of T's = 56,371,392 bp (33.59%) number of G's = 40,709,438 bp (24.26%) number of N's = 8,180 bp (0%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,032,914 number of insertions = 11,008 mapped reads with insertion percentage = 0.4% number of deletions = 49,332 mapped reads with deletion percentage = 1.78% homopolymer indels = 40.18% >>>>>>> Coverage mean coverageData = 0.0542X std coverageData = 0.8505X There is a 2.89% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 23126208 0.09278295037828611 1.4768847613732858 chr2 243199373 18543994 0.07625017191142183 2.0404048931485916 chr3 198022430 6604390 0.03335172687255681 0.315551389244623 chr4 191154276 8339169 0.043625333288385346 0.3575937362075092 chr5 180915260 16821902 0.09298221719936726 0.5257146849754326 chr6 171115067 7752583 0.045306255819074076 0.7188818682488283 chr7 159138663 7211800 0.04531771138481916 0.6032313852027101 chr8 146364022 20102023 0.13734265241768226 0.7549315342094762 chr9 141213431 7105734 0.05031910881054933 0.48103764329767346 chr10 135534747 7423672 0.05477320144331697 0.4914634804768559 chr11 135006516 2429179 0.017993050053969246 0.2359692953570766 chr12 133851895 3877820 0.028970975719096095 0.3070981596751261 chr13 115169878 1109356 0.009632345012990288 0.34981829821344584 chr14 107349540 1935127 0.01802641166417667 0.2657248569667736 chr15 102531392 1980891 0.019319848890767034 0.3830166693439376 chr16 90354753 5724346 0.06335412150371325 0.4663015462209023 chr17 81195210 5802759 0.07146676509611835 0.47821816186334 chr18 78077248 8404715 0.10764614808144878 1.0996306847478945 chr19 59128983 4143601 0.07007732569998709 1.073158135748091 chr20 63025520 3098231 0.0491583568053068 0.3873730588096293 chr21 48129895 1396574 0.02901676806068245 0.3104448076014108 chr22 51304566 1149859 0.02241241062247754 0.2504043864380794 chrMT 16571 20262 1.2227385190996318 1.902851299266844 chrX 155270560 3420798 0.02203120797657972 0.26333026285168326 chrY 59373566 371570 0.00625817219737147 0.2891942322678035