BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093996.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 353,836 number of mapped reads = 340,329 (96.18%) number of supplementary alignments = 22,675 (6.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,085 number of mapped paired reads (second in pair) = 169,244 number of mapped paired reads (both in pair) = 337,314 number of mapped paired reads (singletons) = 3,015 number of mapped bases = 43,721,774 bp number of sequenced bases = 42,913,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 320,203 duplication rate = 50.63% >>>>>>> Insert size mean insert size = 1,229,102.9519 std insert size = 10,041,005.0268 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 40.7118 >>>>>>> ACTG content number of A's = 11,297,092 bp (26.33%) number of C's = 10,097,774 bp (23.53%) number of T's = 10,669,356 bp (24.86%) number of G's = 10,848,770 bp (25.28%) number of N's = 417 bp (0%) GC percentage = 48.81% >>>>>>> Mismatches and indels general error rate = 0.0356 number of mismatches = 1,481,692 number of insertions = 23,067 mapped reads with insertion percentage = 6.66% number of deletions = 116,708 mapped reads with deletion percentage = 32.88% homopolymer indels = 28.09% >>>>>>> Coverage mean coverageData = 0.0141X std coverageData = 2.6145X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% 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 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 849366 0.003407678571039548 1.0968978700806786 chr2 243199373 2231842 0.009177005567362215 2.8002716889080816 chr3 198022430 739881 0.0037363494630381013 1.1836075596550601 chr4 191154276 945258 0.004945000550236187 1.7234397125414087 chr5 180915260 609919 0.0033712965948809403 1.3619296973659072 chr6 171115067 864330 0.005051162443807476 1.3486752442880199 chr7 159138663 903863 0.005679719704569844 1.6451800396594154 chr8 146364022 509980 0.003484326223284572 1.0733636976446743 chr9 141213431 570759 0.00404181809023534 1.1149383662685413 chr10 135534747 631758 0.004661225360903208 1.4361540066463923 chr11 135006516 938039 0.0069481016753295075 1.7498220155058422 chr12 133851895 1211721 0.009052699627450176 2.235511145144877 chr13 115169878 835147 0.007251436004820635 1.9348778710629004 chr14 107349540 194552 0.001812322623832389 0.6172282280032472 chr15 102531392 608560 0.005935352950245716 1.5133095517915396 chr16 90354753 278325 0.0030803581522711927 0.8155147977411706 chr17 81195210 1113983 0.013719811796779637 3.139663927897833 chr18 78077248 195480 0.002503674309832232 0.7134058469447714 chr19 59128983 158528 0.002681054061085407 0.715709207967407 chr20 63025520 357499 0.005672289574128068 1.9064251267922112 chr21 48129895 178482 0.003708339691993926 0.8582299448181206 chr22 51304566 154661 0.003014565993989697 0.718744982884024 chrMT 16571 1024525 61.82638344095106 264.83866751720393 chrX 155270560 27061635 0.17428696721387493 8.818599364438914 chrY 59373566 553681 0.00932537890683541 1.2467359480055418