BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013297.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 = 2,198,919 number of mapped reads = 1,619,592 (73.65%) number of supplementary alignments = 16,237 (0.74%) number of secondary alignments = 0 number of mapped bases = 104,109,486 bp number of sequenced bases = 104,068,119 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 151,720 duplication rate = 7.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2205 >>>>>>> ACTG content number of A's = 27,620,275 bp (26.54%) number of C's = 19,356,479 bp (18.6%) number of T's = 32,965,073 bp (31.68%) number of G's = 24,105,118 bp (23.16%) number of N's = 21,174 bp (0.02%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 914,589 number of insertions = 7,561 mapped reads with insertion percentage = 0.46% number of deletions = 24,787 mapped reads with deletion percentage = 1.52% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.3255X There is a 2.32% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.08% 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% 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 7662986 0.030744099931450122 0.31240708744315315 chr2 243199373 14894510 0.06124403125003122 0.5618576388316802 chr3 198022430 4081858 0.020613109333119484 0.19271248835144084 chr4 191154276 8220846 0.04300634111893997 0.28583948383133156 chr5 180915260 4062279 0.022454042848568993 0.20584943403554437 chr6 171115067 4397818 0.025700939590550493 0.26161377409225656 chr7 159138663 3943843 0.024782431407005097 0.3540288134016592 chr8 146364022 9194385 0.06281861398971395 0.4972243684381577 chr9 141213431 4929277 0.034906573440595744 0.3221412421424849 chr10 135534747 5778816 0.04263715488397968 0.3472723443383812 chr11 135006516 3081705 0.022826342692970465 0.23981524081432526 chr12 133851895 4053472 0.030283261959048097 0.24587575881654247 chr13 115169878 1060566 0.009208709937159089 0.1328171017143186 chr14 107349540 3047930 0.028392576251374715 0.24918967134683156 chr15 102531392 1054499 0.010284645311359862 0.1533074739554028 chr16 90354753 5159232 0.05709972999428154 0.3396397471848238 chr17 81195210 5651515 0.0696040443765094 0.42199272045418057 chr18 78077248 2278775 0.029186159327746798 0.47456551709658795 chr19 59128983 1399813 0.02367388933444027 0.3131664910728318 chr20 63025520 1737390 0.027566452446564502 0.23338826140511754 chr21 48129895 2283447 0.04744342367669824 0.3065162707204802 chr22 51304566 1089208 0.02123023514125429 0.19879306276505304 chrMT 16571 59825 3.610222678172711 3.294565154985767 chrX 155270560 4759942 0.030655792057425437 0.2619457984082381 chrY 59373566 225549 0.003798811747301821 0.08251019795875546