BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089719.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 13,875,704 number of mapped reads = 11,966,955 (86.24%) number of supplementary alignments = 653 (0%) number of secondary alignments = 0 number of mapped bases = 565,832,512 bp number of sequenced bases = 565,714,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,818,740 duplication rate = 11.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5758 >>>>>>> ACTG content number of A's = 169,055,185 bp (29.88%) number of C's = 110,080,766 bp (19.46%) number of T's = 171,728,992 bp (30.36%) number of G's = 114,844,219 bp (20.3%) number of N's = 5,645 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 2,922,996 number of insertions = 26,119 mapped reads with insertion percentage = 0.22% number of deletions = 77,744 mapped reads with deletion percentage = 0.65% homopolymer indels = 49.6% >>>>>>> Coverage mean coverageData = 0.1828X std coverageData = 1.225X There is a 10.2% of reference with a coverageData >= 1X There is a 4.03% of reference with a coverageData >= 2X There is a 1.83% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 44663491 0.17919109216582454 2.235834584998757 chr2 243199373 48007974 0.19740171780788268 1.1045988539912912 chr3 198022430 39260980 0.19826531772183587 0.7256268841547375 chr4 191154276 38348280 0.20061429334701358 0.7732662683276137 chr5 180915260 35062784 0.19380777497708043 0.7327136734178913 chr6 171115067 33516849 0.19587316060250848 0.8914467491786977 chr7 159138663 31271279 0.19650334124021138 1.678478226960095 chr8 146364022 29866992 0.20405965613598676 2.0257944119979223 chr9 141213431 23541982 0.16671206012974785 1.0411063664501523 chr10 135534747 25723597 0.18979337453590406 1.0256269641847475 chr11 135006516 26398127 0.1955322437918478 1.085310963098592 chr12 133851895 25309328 0.18908456992708247 0.7912950494411803 chr13 115169878 18325212 0.15911462544051666 0.6507546248558465 chr14 107349540 17253491 0.16072254245337242 0.7249529835101691 chr15 102531392 15483910 0.15101628582200463 0.6313976156823627 chr16 90354753 14914090 0.16506148824290406 0.7150627112788992 chr17 81195210 13557419 0.16697313794742324 0.7827837294825946 chr18 78077248 15319934 0.19621508688420986 2.3314803585970574 chr19 59128983 9750323 0.1648992170218791 1.6524894343281895 chr20 63025520 11698975 0.18562282389736728 0.7904472888177783 chr21 48129895 7271106 0.15107255064653682 0.7411837212995294 chr22 51304566 5544576 0.10807178448795376 0.5181289298232219 chrMT 16571 66217 3.9959567919859995 3.512219765688291 chrX 155270560 34088725 0.21954403333123806 0.9446976468488393 chrY 59373566 1586871 0.026726893917741103 0.49479506174062554