BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237858.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 = 3,498,110 number of mapped reads = 2,957,321 (84.54%) number of supplementary alignments = 29,018 (0.83%) number of secondary alignments = 0 number of mapped bases = 193,256,906 bp number of sequenced bases = 193,176,962 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,545 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3703 >>>>>>> ACTG content number of A's = 55,021,024 bp (28.48%) number of C's = 36,705,515 bp (19%) number of T's = 59,357,565 bp (30.73%) number of G's = 41,914,197 bp (21.7%) number of N's = 178,661 bp (0.09%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,652,764 number of insertions = 17,798 mapped reads with insertion percentage = 0.6% number of deletions = 46,494 mapped reads with deletion percentage = 1.55% homopolymer indels = 45.6% >>>>>>> Coverage mean coverageData = 0.0624X std coverageData = 0.7599X There is a 5.23% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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% 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 21375963 0.08576092173507564 1.5751245801616323 chr2 243199373 10097315 0.041518672007431534 0.6366268438388216 chr3 198022430 13352523 0.06742934626143109 0.38112232420135117 chr4 191154276 5096932 0.0266639706244395 0.32330993595094204 chr5 180915260 12899642 0.07130212233064254 0.3041550193557443 chr6 171115067 5756251 0.03363965021268408 0.2635939883877027 chr7 159138663 13995451 0.08794500805878959 1.3818316790634406 chr8 146364022 9345125 0.06384851189727486 0.7397486577628438 chr9 141213431 4023821 0.028494605445851678 0.48450329385098334 chr10 135534747 11970164 0.08831804585137124 1.3574262261153298 chr11 135006516 6988963 0.05176759764691654 0.4617379765922975 chr12 133851895 12019985 0.08980063375270107 0.34424716155466584 chr13 115169878 6779314 0.05886360320708163 0.26845739511561734 chr14 107349540 6432146 0.05991777887450659 0.3195351154812638 chr15 102531392 3715544 0.036238111348376116 0.21268650275868647 chr16 90354753 5138715 0.05687265837581339 0.3971056147267297 chr17 81195210 5053972 0.06224470630718241 0.4509695819793989 chr18 78077248 3891206 0.04983789899971884 1.0861568851538839 chr19 59128983 3559564 0.06019998686600106 1.038117208521737 chr20 63025520 4736978 0.07515968134812692 0.34092320747700844 chr21 48129895 2216656 0.046055699892966734 0.30866299744503295 chr22 51304566 1100233 0.021445128295208657 0.16505950224919638 chrMT 16571 165218 9.970309576971818 6.829469787762706 chrX 155270560 22741512 0.14646377265593682 0.5517442693773639 chrY 59373566 803713 0.013536545876324827 0.3061962096147028