BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013160.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 = 3,847,387 number of mapped reads = 2,956,524 (76.84%) number of supplementary alignments = 26,360 (0.69%) number of secondary alignments = 0 number of mapped bases = 191,377,748 bp number of sequenced bases = 191,267,057 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 485,866 duplication rate = 11.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.614 >>>>>>> ACTG content number of A's = 51,476,439 bp (26.91%) number of C's = 35,249,578 bp (18.43%) number of T's = 60,476,793 bp (31.62%) number of G's = 43,769,329 bp (22.88%) number of N's = 294,918 bp (0.15%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,755,942 number of insertions = 13,018 mapped reads with insertion percentage = 0.44% number of deletions = 64,246 mapped reads with deletion percentage = 2.14% homopolymer indels = 44.43% >>>>>>> Coverage mean coverageData = 0.0618X std coverageData = 0.6201X There is a 2.99% of reference with a coverageData >= 1X There is a 1.38% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 15241325 0.06114859388855846 0.9226887326581428 chr2 243199373 15912863 0.06543134878888031 0.9007009083846531 chr3 198022430 13030607 0.06580369203630114 0.4665816889657816 chr4 191154276 13035654 0.06819441486100997 0.4844795369044841 chr5 180915260 12807866 0.07079483510677873 0.48462618650939765 chr6 171115067 12436504 0.07267918727460744 0.5614189850475614 chr7 159138663 11628845 0.07307366280939535 0.8413825714756733 chr8 146364022 10115403 0.0691112669751587 0.679087684319265 chr9 141213431 8110625 0.05743522370758062 0.5960428815150284 chr10 135534747 7379845 0.05444983787072698 0.5636075471664775 chr11 135006516 8610887 0.0637812696388669 0.5261405749592257 chr12 133851895 7640592 0.05708243428305591 0.4386091162123041 chr13 115169878 6505916 0.056489735970719705 0.4362184061758583 chr14 107349540 5643718 0.05257328536293682 0.43535718273261304 chr15 102531392 3954055 0.03856433549639119 0.35503447935501525 chr16 90354753 5077248 0.05619237318926654 0.456481895187785 chr17 81195210 5402281 0.0665344790659449 0.4972030606730001 chr18 78077248 6453322 0.08265304125473275 0.8582918248364048 chr19 59128983 3570943 0.060392430561506526 0.724643253692034 chr20 63025520 5389424 0.0855117736434384 0.5532189974234936 chr21 48129895 2730660 0.05673521623099323 0.4481018574341104 chr22 51304566 1908741 0.03720411551673588 0.34620256380172837 chrMT 16571 368322 22.22690241989017 13.660670224079583 chrX 155270560 7838193 0.050480870295051425 0.42637720961596726 chrY 59373566 583909 0.009834494360672222 0.19927649675084846