BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084383.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,401,588 number of mapped reads = 1,266,012 (90.33%) number of supplementary alignments = 7,533 (0.54%) number of secondary alignments = 0 number of mapped bases = 86,858,690 bp number of sequenced bases = 86,826,575 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,614 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0025 >>>>>>> ACTG content number of A's = 25,185,749 bp (29.01%) number of C's = 15,962,625 bp (18.38%) number of T's = 27,583,373 bp (31.77%) number of G's = 17,981,493 bp (20.71%) number of N's = 113,335 bp (0.13%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 862,636 number of insertions = 6,314 mapped reads with insertion percentage = 0.49% number of deletions = 18,585 mapped reads with deletion percentage = 1.45% homopolymer indels = 48.17% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.2405X There is a 2.53% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 8540947 0.03426650238917559 0.4101988956030493 chr2 243199373 8682264 0.035700190723764735 0.24717515081472696 chr3 198022430 5751893 0.029046674157063926 0.18947456793640394 chr4 191154276 4400349 0.023019882641809174 0.16806347398992907 chr5 180915260 4632269 0.025604633904293093 0.1727523918639797 chr6 171115067 4290461 0.025073543056264004 0.18160674924045134 chr7 159138663 5143715 0.03232222077924583 0.32086340043748857 chr8 146364022 2973316 0.020314527842094966 0.27777097483589025 chr9 141213431 3272914 0.02317707300802004 0.19139548654639518 chr10 135534747 6080834 0.04486549858686791 0.3486307836529257 chr11 135006516 4929535 0.03651331169822944 0.24111542717101922 chr12 133851895 4545447 0.03395877958993408 0.19956311731714776 chr13 115169878 2315378 0.020104024074767187 0.15231480793954585 chr14 107349540 2351900 0.02190880370796186 0.16230506284608498 chr15 102531392 1845659 0.018000916246216574 0.14420742266991513 chr16 90354753 1766748 0.019553459462171293 0.16118613368523294 chr17 81195210 2207936 0.027192934164466106 0.18544947907060383 chr18 78077248 2517465 0.03224325990588193 0.3065335612934433 chr19 59128983 1593017 0.026941390147028236 0.27050433048140454 chr20 63025520 1689598 0.026808156442025388 0.17823436895207 chr21 48129895 892698 0.018547682266915395 0.14982316082398153 chr22 51304566 649053 0.01265097925202213 0.12011115364184986 chrMT 16571 2796 0.1687285015991793 0.4635162675110135 chrX 155270560 5595113 0.036034603082516097 0.2178588873724964 chrY 59373566 187385 0.003156034117944002 0.07939037976195101