BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068114.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 = 1,418,555 number of mapped reads = 650,242 (45.84%) number of supplementary alignments = 4,770 (0.34%) number of secondary alignments = 0 number of mapped bases = 40,584,637 bp number of sequenced bases = 40,568,869 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 134,961 duplication rate = 12.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7823 >>>>>>> ACTG content number of A's = 10,647,107 bp (26.24%) number of C's = 7,163,652 bp (17.66%) number of T's = 13,148,380 bp (32.41%) number of G's = 9,573,411 bp (23.6%) number of N's = 36,319 bp (0.09%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 387,413 number of insertions = 3,036 mapped reads with insertion percentage = 0.46% number of deletions = 9,587 mapped reads with deletion percentage = 1.46% homopolymer indels = 46.16% >>>>>>> Coverage mean coverageData = 0.0131X std coverageData = 0.2976X There is a 0.61% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% 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 3420456 0.013722958788535976 0.3016159514739189 chr2 243199373 4157150 0.01709358847730253 0.3619573671340705 chr3 198022430 2417132 0.012206354603364881 0.2365207954315978 chr4 191154276 2565939 0.013423393154961388 0.4153654932882492 chr5 180915260 2070496 0.011444562498486861 0.22474010451475124 chr6 171115067 2215182 0.012945569544732142 0.2817569428124931 chr7 159138663 2270884 0.014269844657423068 0.2814350687654696 chr8 146364022 2019154 0.01379542576385336 0.27732403640785785 chr9 141213431 1518461 0.010752950262925061 0.2375623964175833 chr10 135534747 1896694 0.013994153100828084 0.2781143294719074 chr11 135006516 1766517 0.013084679557244482 0.24456003579524035 chr12 133851895 1950980 0.014575662152560485 0.2587856210301878 chr13 115169878 1230101 0.010680752826706998 0.24298852670723226 chr14 107349540 1227816 0.011437552503718227 0.28965277024043473 chr15 102531392 1216358 0.011863274030259923 0.553722529161846 chr16 90354753 995952 0.011022685215021285 0.23119568524750356 chr17 81195210 1148848 0.014149209048169221 0.24460953163387078 chr18 78077248 1468994 0.01881462317934157 0.3396142399022707 chr19 59128983 837043 0.014156221831178798 0.304997818711263 chr20 63025520 803541 0.012749454506682372 0.2515180958521181 chr21 48129895 512655 0.010651488020075673 0.21096409567068727 chr22 51304566 431983 0.008419971820831698 0.20785652846656927 chrMT 16571 17304 1.0442339026009293 2.2288866846089666 chrX 155270560 2306556 0.014855076197316477 0.28348114701244653 chrY 59373566 118441 0.0019948439681052674 0.13489047196189272