BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238251.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 = 1,202,158 number of mapped reads = 810,179 (67.39%) number of supplementary alignments = 8,359 (0.7%) number of secondary alignments = 0 number of mapped bases = 50,982,764 bp number of sequenced bases = 50,959,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,372 duplication rate = 7.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.052 >>>>>>> ACTG content number of A's = 14,321,719 bp (28.1%) number of C's = 9,984,168 bp (19.59%) number of T's = 15,455,893 bp (30.33%) number of G's = 11,187,347 bp (21.95%) number of N's = 10,569 bp (0.02%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 464,647 number of insertions = 4,149 mapped reads with insertion percentage = 0.51% number of deletions = 14,123 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.0165X std coverageData = 0.2458X There is a 1.04% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.06% 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 4938241 0.019812351841642956 0.27756513507671404 chr2 243199373 4654011 0.019136607724724686 0.32528389869167756 chr3 198022430 3619896 0.01828023219389844 0.20875158338889374 chr4 191154276 2615663 0.013683518123340333 0.19982614562305095 chr5 180915260 3279206 0.018125646227963303 0.21264429833378098 chr6 171115067 2209320 0.012911311895170518 0.21661157770056907 chr7 159138663 2331100 0.014648231649401253 0.23451767439523252 chr8 146364022 2578896 0.01761973991121944 0.24699941733635322 chr9 141213431 1916786 0.013573680537512045 0.1927788388841731 chr10 135534747 1871156 0.013805729094694809 0.1992497225337457 chr11 135006516 1904101 0.014103771109832951 0.2055527740493058 chr12 133851895 2113948 0.015793186939938354 0.2046006395259367 chr13 115169878 1685385 0.014633904535350815 0.21614912250598256 chr14 107349540 1535223 0.014301160489369587 0.35426047751857104 chr15 102531392 1127425 0.010995900650602696 0.3812347958486425 chr16 90354753 1697831 0.018790721501944673 0.2116288317562285 chr17 81195210 990741 0.012201963638002784 0.17998613300843513 chr18 78077248 1468518 0.01880852665298859 0.25579894796858427 chr19 59128983 681424 0.011524365301530724 0.18800782617438277 chr20 63025520 1073564 0.0170337983724688 0.20366619250389192 chr21 48129895 443801 0.009220901063673627 0.14442712151293818 chr22 51304566 917314 0.01787977311804957 0.19960907104019057 chrMT 16571 40158 2.4233902600929333 2.7179530340028064 chrX 155270560 5112778 0.03292818677281772 0.3203524068971462 chrY 59373566 176278 0.0029689643367555186 0.08400274415711491