BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013162.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 = 2,813,089 number of mapped reads = 2,139,333 (76.05%) number of supplementary alignments = 18,838 (0.67%) number of secondary alignments = 0 number of mapped bases = 137,693,872 bp number of sequenced bases = 137,612,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 642,821 duplication rate = 15.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.781 >>>>>>> ACTG content number of A's = 35,531,171 bp (25.82%) number of C's = 26,785,878 bp (19.46%) number of T's = 41,991,329 bp (30.51%) number of G's = 33,088,093 bp (24.04%) number of N's = 215,939 bp (0.16%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,303,693 number of insertions = 10,709 mapped reads with insertion percentage = 0.5% number of deletions = 44,077 mapped reads with deletion percentage = 2.03% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0445X std coverageData = 0.7037X There is a 1.09% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.18% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 10062553 0.0403712253940583 0.7441371124936159 chr2 243199373 13192261 0.054244634092868324 0.9453929793851551 chr3 198022430 9337735 0.047154935933267764 0.6703154563552711 chr4 191154276 8117392 0.04246513428765779 0.6392689004767569 chr5 180915260 7080737 0.03913841762159809 0.6047707002046188 chr6 171115067 6789126 0.03967579313164749 0.6362104708760099 chr7 159138663 7675390 0.048230831246835346 0.7056280581420292 chr8 146364022 7053290 0.04819005315390964 0.7138415647474095 chr9 141213431 5267477 0.03730152976737744 0.605212599486916 chr10 135534747 6655288 0.049103924619418815 0.7218773180629755 chr11 135006516 5689199 0.04214018084875251 0.6390676881714406 chr12 133851895 7379447 0.05513143463527356 0.7345282563176077 chr13 115169878 3138150 0.027248010109032154 0.5018627652169093 chr14 107349540 4394227 0.04093382235266215 0.6081399905997388 chr15 102531392 4530835 0.04418973459367449 0.6455040164634307 chr16 90354753 4678066 0.05177443183315437 0.6895173511489995 chr17 81195210 4300771 0.05296828470546477 0.7009690186563652 chr18 78077248 3684835 0.047194734629991054 0.7798939822130269 chr19 59128983 3403925 0.05756779209275424 0.7775648160299063 chr20 63025520 3421514 0.05428775518234518 0.7261329274252575 chr21 48129895 2136831 0.044397167290724404 0.651534605807599 chr22 51304566 1927565 0.03757102243102495 0.5958406048212411 chrMT 16571 720046 43.45217548729708 41.462799086187594 chrX 155270560 6555839 0.042222034878988006 0.6091821406649421 chrY 59373566 501373 0.008444380787234508 0.2747897524491364