BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238267.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 = 3,233,997 number of mapped reads = 2,914,058 (90.11%) number of supplementary alignments = 35,725 (1.1%) number of secondary alignments = 0 number of mapped bases = 190,876,250 bp number of sequenced bases = 190,755,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,379 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4785 >>>>>>> ACTG content number of A's = 53,159,345 bp (27.87%) number of C's = 36,744,990 bp (19.26%) number of T's = 58,407,935 bp (30.62%) number of G's = 42,380,007 bp (22.22%) number of N's = 62,856 bp (0.03%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,776,905 number of insertions = 15,435 mapped reads with insertion percentage = 0.53% number of deletions = 73,133 mapped reads with deletion percentage = 2.48% homopolymer indels = 44.25% >>>>>>> Coverage mean coverageData = 0.0617X std coverageData = 0.5757X There is a 4.98% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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% 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 18595480 0.07460555133381193 1.2086134310418863 chr2 243199373 11235997 0.04620076467055694 0.708921289733537 chr3 198022430 16809298 0.08488582833772922 0.344229957181149 chr4 191154276 11553548 0.060440960263949316 0.3053343781167025 chr5 180915260 13993881 0.07735047336526504 0.33372036572275093 chr6 171115067 10670989 0.062361481002721986 0.45987050332533014 chr7 159138663 9020648 0.05668420124907044 0.6000499230661729 chr8 146364022 8990740 0.06142725430160699 0.8200810857567038 chr9 141213431 5045557 0.03573000786306226 0.4675495263041754 chr10 135534747 8618406 0.0635881660663741 0.5471688795433223 chr11 135006516 6118616 0.04532089399299809 0.3705347470787847 chr12 133851895 10945307 0.08177177469172177 0.3471832297841808 chr13 115169878 3700041 0.03212681183876916 0.2129100710842593 chr14 107349540 4494137 0.04186452033236472 0.2659069120700862 chr15 102531392 5913139 0.057671498305611614 0.2897344282642537 chr16 90354753 4789917 0.05301234125447723 0.3129553396461238 chr17 81195210 5463591 0.06728957287012374 0.36446086154101803 chr18 78077248 8378971 0.10731642334524906 0.8557905827689335 chr19 59128983 4310541 0.07290064501870427 0.8377312093328441 chr20 63025520 5252053 0.08333216449463646 0.3496138968152352 chr21 48129895 2928115 0.06083775998264696 0.308036710928183 chr22 51304566 2734334 0.053296114033982864 0.27225635720663277 chrMT 16571 10881 0.6566290507513125 0.9409713479992073 chrX 155270560 10793132 0.06951177351327902 0.3706469430453249 chrY 59373566 508931 0.008571676493205747 0.19480593771606194