BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238250.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 = 3,430,638 number of mapped reads = 3,014,364 (87.87%) number of supplementary alignments = 31,021 (0.9%) number of secondary alignments = 0 number of mapped bases = 195,658,506 bp number of sequenced bases = 195,569,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 171,147 duplication rate = 4.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1596 >>>>>>> ACTG content number of A's = 55,252,253 bp (28.25%) number of C's = 37,120,887 bp (18.98%) number of T's = 60,457,019 bp (30.91%) number of G's = 42,689,644 bp (21.83%) number of N's = 49,366 bp (0.03%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,738,693 number of insertions = 15,908 mapped reads with insertion percentage = 0.52% number of deletions = 54,262 mapped reads with deletion percentage = 1.78% homopolymer indels = 45.21% >>>>>>> Coverage mean coverageData = 0.0632X std coverageData = 0.6419X There is a 4.87% of reference with a coverageData >= 1X There is a 0.97% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 20872335 0.08374035304810735 1.1754385080420677 chr2 243199373 10761386 0.04424923414584626 0.5452823218347068 chr3 198022430 18113593 0.09147243067363632 0.379114272545802 chr4 191154276 10284974 0.0538045719678277 0.31565618884382557 chr5 180915260 12875521 0.07116879471637716 0.33071364168027484 chr6 171115067 15213276 0.08890670042515894 0.8188911587213328 chr7 159138663 13722367 0.08622899514997182 1.1221853246761497 chr8 146364022 7077719 0.04835695892532934 1.0474473955261276 chr9 141213431 4990526 0.035340306971225706 0.34196161689443316 chr10 135534747 7367846 0.054361307067625986 0.6111910431952277 chr11 135006516 11012745 0.08157195168268767 0.49105732959950155 chr12 133851895 15244019 0.11388721093563897 0.42357555193249896 chr13 115169878 5781043 0.05019578990958035 0.277242401697121 chr14 107349540 8300969 0.0773265446689385 0.36524771271570433 chr15 102531392 2654760 0.025892167737272112 0.2303897967374166 chr16 90354753 4367965 0.04834239323303778 0.32824619088360313 chr17 81195210 1310240 0.016136912509986733 0.20224438081608898 chr18 78077248 4137984 0.05299858929454071 0.9593214714578444 chr19 59128983 1923251 0.03252636697641155 0.8219629854496037 chr20 63025520 3599156 0.05710632772248448 0.3146421655470022 chr21 48129895 4133330 0.0858786415386944 0.39095251546197246 chr22 51304566 2494660 0.04862452203571901 0.2705718251036624 chrMT 16571 18526 1.1179771890652344 1.474636905142283 chrX 155270560 8860404 0.05706428829779451 0.33654706037183585 chrY 59373566 539911 0.009093457516093946 0.17812419933741028