BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063528.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 = 5,536,827 number of mapped reads = 5,252,569 (94.87%) number of supplementary alignments = 31,817 (0.57%) number of secondary alignments = 0 number of mapped bases = 338,143,744 bp number of sequenced bases = 337,999,061 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 662,894 duplication rate = 10.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9241 >>>>>>> ACTG content number of A's = 86,666,012 bp (25.64%) number of C's = 61,282,899 bp (18.13%) number of T's = 109,543,286 bp (32.41%) number of G's = 80,469,297 bp (23.81%) number of N's = 37,567 bp (0.01%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,779,649 number of insertions = 20,234 mapped reads with insertion percentage = 0.38% number of deletions = 82,558 mapped reads with deletion percentage = 1.56% homopolymer indels = 44.61% >>>>>>> Coverage mean coverageData = 0.1092X std coverageData = 1.3461X There is a 8% of reference with a coverageData >= 1X There is a 1.93% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 34828443 0.13973262277248247 3.6557638309937617 chr2 243199373 35895407 0.14759662641071036 1.7964406692648374 chr3 198022430 15609884 0.07882886802267804 0.3713023136680885 chr4 191154276 14089282 0.0737063396897279 0.3766275899501239 chr5 180915260 16890981 0.09336404789734155 0.40841137918126635 chr6 171115067 29356283 0.1715587266199066 0.8442558331550475 chr7 159138663 33458573 0.2102479207079929 1.5391896843770734 chr8 146364022 10837597 0.07404549869502766 0.6278249034040692 chr9 141213431 12687200 0.08984414520740594 0.7476889491813309 chr10 135534747 20835488 0.15372801780491022 0.7700593891290902 chr11 135006516 15371881 0.11386028952854393 0.5833159002779926 chr12 133851895 11268940 0.08418961868264921 0.4311291569119614 chr13 115169878 7333087 0.06367191775613412 0.3926770571607747 chr14 107349540 8428568 0.07851517575203397 0.4403848277724984 chr15 102531392 7203202 0.07025362534822506 0.4132329347168506 chr16 90354753 8469542 0.09373654089896079 0.4671824887089514 chr17 81195210 9556530 0.11769819919179962 0.4928094978342534 chr18 78077248 6960194 0.0891449708883182 1.4787323951682965 chr19 59128983 8287677 0.14016268468544435 2.1370786902552035 chr20 63025520 4478111 0.07105234514526813 0.4134212113687943 chr21 48129895 6793868 0.14115692544103825 0.5083903123859144 chr22 51304566 4130367 0.08050681103120529 0.3639572258175529 chrMT 16571 125167 7.553376380423631 5.135472451942046 chrX 155270560 14613089 0.09411371350757027 0.542418303763765 chrY 59373566 634383 0.010684603313198334 0.23798897354413107