BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013265.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 = 1,697,623 number of mapped reads = 1,539,224 (90.67%) number of supplementary alignments = 7,050 (0.42%) number of secondary alignments = 0 number of mapped bases = 102,999,956 bp number of sequenced bases = 102,956,536 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,274 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8719 >>>>>>> ACTG content number of A's = 28,576,809 bp (27.76%) number of C's = 18,713,975 bp (18.18%) number of T's = 32,987,510 bp (32.04%) number of G's = 22,655,857 bp (22.01%) number of N's = 22,385 bp (0.02%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 811,529 number of insertions = 7,485 mapped reads with insertion percentage = 0.48% number of deletions = 25,498 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.79% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.319X There is a 2.94% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 7353228 0.029501342746905333 0.44059314395676813 chr2 243199373 10935827 0.04496650984375688 0.4170555081380631 chr3 198022430 7494405 0.03784624297358637 0.21311584765126376 chr4 191154276 7817363 0.04089556960787003 0.22687669624668938 chr5 180915260 4587287 0.025355998161791328 0.17503353491204765 chr6 171115067 6347990 0.03709778519971009 0.27120612090528284 chr7 159138663 6377430 0.04007467374537387 0.6541379699369471 chr8 146364022 6848602 0.0467915673976218 0.38903774449218437 chr9 141213431 4047263 0.028660609485509917 0.267592483954311 chr10 135534747 3929937 0.02899578954465455 0.30161786380958877 chr11 135006516 4197575 0.031091647457964177 0.2335746382174143 chr12 133851895 5206918 0.03890059233005255 0.2200877263670871 chr13 115169878 2305317 0.020016666163352192 0.15714098200389823 chr14 107349540 4032952 0.037568414359297676 0.22822403945853803 chr15 102531392 1820976 0.017760180218756808 0.14747771505542231 chr16 90354753 2577039 0.028521344084688052 0.20421727309730722 chr17 81195210 3026409 0.03727324555229305 0.2211080608352297 chr18 78077248 2859378 0.03662242296244868 0.520575939664986 chr19 59128983 1517021 0.02565613212052032 0.35870910899026004 chr20 63025520 1831700 0.02906283042170854 0.18997530388492864 chr21 48129895 1615453 0.03356444056235735 0.2080383894179861 chr22 51304566 1202319 0.023434931697892153 0.16766948273738724 chrMT 16571 66991 4.042664896505944 3.122005074529673 chrX 155270560 4824913 0.031074229396738182 0.21003244807883253 chrY 59373566 175663 0.002958606191853122 0.07764511254523458