BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063527.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 = 2,884,984 number of mapped reads = 2,567,291 (88.99%) number of supplementary alignments = 25,637 (0.89%) number of secondary alignments = 0 number of mapped bases = 158,025,944 bp number of sequenced bases = 157,945,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 579,407 duplication rate = 17.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1428 >>>>>>> ACTG content number of A's = 40,004,770 bp (25.33%) number of C's = 27,048,302 bp (17.13%) number of T's = 53,316,066 bp (33.76%) number of G's = 37,560,868 bp (23.78%) number of N's = 15,835 bp (0.01%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,020,934 number of insertions = 11,049 mapped reads with insertion percentage = 0.43% number of deletions = 46,408 mapped reads with deletion percentage = 1.79% homopolymer indels = 41.68% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.7035X There is a 2.91% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 13315124 0.05342062517870316 0.9267301832458452 chr2 243199373 14717194 0.06051493397559047 1.5785998925610871 chr3 198022430 9951973 0.05025679666692304 0.3639568652740301 chr4 191154276 12245013 0.0640582740613137 0.4832781300098151 chr5 180915260 8033753 0.04440616562693495 0.3444362452057396 chr6 171115067 10218793 0.059718838201430854 0.6338224234939372 chr7 159138663 7714410 0.04847602621871971 0.6072075324610865 chr8 146364022 7808127 0.053347310994227806 0.6444339889236185 chr9 141213431 7090291 0.05020974952446273 0.5447331848181581 chr10 135534747 7645477 0.05640971905160232 0.6023961040084086 chr11 135006516 7404540 0.05484579722063193 0.4976334115787582 chr12 133851895 7994297 0.05972494449929155 0.42291992469931167 chr13 115169878 4816551 0.04182127378827301 0.39189674995409035 chr14 107349540 4238403 0.03948226513127117 0.3520657078938146 chr15 102531392 4907339 0.047861819724441076 0.3900849124147941 chr16 90354753 3196644 0.035378813995540444 0.3580055818509276 chr17 81195210 3658292 0.04505551497434393 0.37859104919038833 chr18 78077248 4584735 0.05872049947252239 1.3237410537290966 chr19 59128983 2327101 0.03935635084405223 0.5718364421816625 chr20 63025520 2796234 0.04436669463417359 0.36934295090275376 chr21 48129895 1929285 0.0400849617477869 0.37018169919467847 chr22 51304566 1662223 0.03239912408575876 0.287004616228803 chrMT 16571 87784 5.297447347776235 4.366112801482684 chrX 155270560 9096115 0.058582354568696086 0.42818311797332104 chrY 59373566 586246 0.00987385531130133 0.36944428206719615