BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238249.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 = 2,902,818 number of mapped reads = 2,591,942 (89.29%) number of supplementary alignments = 23,924 (0.82%) number of secondary alignments = 0 number of mapped bases = 168,140,703 bp number of sequenced bases = 168,055,042 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,194 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.686 >>>>>>> ACTG content number of A's = 46,620,252 bp (27.74%) number of C's = 32,714,424 bp (19.47%) number of T's = 50,939,205 bp (30.31%) number of G's = 37,741,531 bp (22.46%) number of N's = 39,630 bp (0.02%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,494,315 number of insertions = 13,086 mapped reads with insertion percentage = 0.5% number of deletions = 52,003 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.68% >>>>>>> Coverage mean coverageData = 0.0543X std coverageData = 0.4288X There is a 4.53% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 20231740 0.08117026918059314 0.7120221646805556 chr2 243199373 16235059 0.06675617128338567 0.6338004895747057 chr3 198022430 11733412 0.05925294422455073 0.283650661176345 chr4 191154276 8050214 0.042113700872691964 0.2515187459579555 chr5 180915260 10134829 0.05601975753731332 0.27388818291422046 chr6 171115067 12080527 0.07059885030463156 0.4377780996436803 chr7 159138663 7603876 0.04778144956515061 0.5035642412583686 chr8 146364022 8159176 0.05574577610336508 0.5466932743950322 chr9 141213431 6823758 0.048322301580506176 0.37646868059537913 chr10 135534747 7512644 0.0554296530320745 0.4267558892217603 chr11 135006516 7404327 0.05484421951900455 0.391657886070409 chr12 133851895 4381046 0.03273054893993096 0.21414023955685543 chr13 115169878 2215924 0.019240482307361653 0.16311495801357348 chr14 107349540 3568901 0.03324561055408342 0.2299814550600956 chr15 102531392 3957900 0.03860183620641764 0.2393320744640514 chr16 90354753 4506860 0.04987961175656139 0.2929285645766594 chr17 81195210 4755607 0.05857004372548578 0.31722437361398 chr18 78077248 4941265 0.06328687455787377 0.5977675258411833 chr19 59128983 2333465 0.03946397995717261 0.585106002743634 chr20 63025520 4793701 0.07605968185585775 0.32213544551949547 chr21 48129895 1863564 0.03871946946902751 0.24278374836996347 chr22 51304566 2448225 0.04771943690158104 0.2553239939445128 chrMT 16571 3725 0.2247902963007664 0.5002627833299463 chrX 155270560 11963137 0.07704703969638546 0.3722224582510075 chrY 59373566 437821 0.007374005462296134 0.15028080615005482