BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004021.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 = 3,193,115 number of mapped reads = 2,713,725 (84.99%) number of supplementary alignments = 28,390 (0.89%) number of secondary alignments = 0 number of mapped bases = 179,464,218 bp number of sequenced bases = 179,358,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 206,913 duplication rate = 5.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4462 >>>>>>> ACTG content number of A's = 50,199,472 bp (27.99%) number of C's = 32,462,965 bp (18.1%) number of T's = 57,540,228 bp (32.08%) number of G's = 39,058,667 bp (21.78%) number of N's = 97,061 bp (0.05%) GC percentage = 39.88% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 1,583,996 number of insertions = 13,612 mapped reads with insertion percentage = 0.5% number of deletions = 62,399 mapped reads with deletion percentage = 2.27% homopolymer indels = 44.98% >>>>>>> Coverage mean coverageData = 0.058X std coverageData = 0.5625X There is a 4.21% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.29% 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 0.01% 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 13794772 0.055344985479494554 1.1351415673089456 chr2 243199373 13301945 0.05469563854508786 0.5436972910457767 chr3 198022430 11585483 0.05850591268877975 0.3133286227496987 chr4 191154276 11261451 0.05891289086308485 0.33880377376136384 chr5 180915260 10654973 0.05889482733518444 0.32306958046788953 chr6 171115067 10627060 0.062104759015756336 0.37922850320880136 chr7 159138663 11134236 0.06996562488400446 0.6061990017246098 chr8 146364022 13473549 0.09205506118163383 0.9705027813558593 chr9 141213431 7231205 0.05120762911001008 0.49604824658298957 chr10 135534747 8288269 0.06115235527019503 0.4430117260609975 chr11 135006516 7158366 0.05302237412007581 0.43538464022186374 chr12 133851895 8016330 0.05988955180649478 0.3356933891841455 chr13 115169878 5023598 0.04361902684311257 0.27223150502637317 chr14 107349540 3640025 0.033908156476497246 0.2739842880192884 chr15 102531392 4809621 0.04690876526868961 0.2849543585852281 chr16 90354753 4338151 0.04801242719350912 0.3320065295329365 chr17 81195210 4948252 0.06094265905587288 0.34846225388854046 chr18 78077248 5003094 0.0640787697845088 0.9910608241944858 chr19 59128983 2794524 0.047261492726840916 0.7082726204849906 chr20 63025520 3366974 0.05342239143762717 0.3140969935816519 chr21 48129895 2659879 0.05526459178853393 0.33398836433485724 chr22 51304566 1974717 0.0384900829294609 0.24756444069843672 chrMT 16571 24645 1.487236738881178 1.7702477596721247 chrX 155270560 13851581 0.08920931952586504 0.47487429369982587 chrY 59373566 501518 0.008446822951479789 0.1651969634583313