BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548919.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,436,716 number of mapped reads = 6,465,474 (86.94%) number of secondary alignments = 0 number of mapped bases = 255,873,651 bp number of sequenced bases = 255,845,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 220,859 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5996 >>>>>>> ACTG content number of A's = 74,261,984 bp (29.03%) number of C's = 53,338,300 bp (20.85%) number of T's = 74,954,839 bp (29.3%) number of G's = 53,288,013 bp (20.83%) number of N's = 2,700 bp (0%) GC percentage = 41.68% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 693,093 number of insertions = 8,372 mapped reads with insertion percentage = 0.13% number of deletions = 20,962 mapped reads with deletion percentage = 0.32% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.0827X std coverageData = 0.8906X There is a 6.81% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 20229456 0.08116110571295226 0.892849532853379 chr2 243199373 21624487 0.08891670538969687 0.47522073745755006 chr3 198022430 17233128 0.08702614143256397 0.3449650326652511 chr4 191154276 16751577 0.0876338073651044 0.35630402231565184 chr5 180915260 15858283 0.08765586164483859 0.34938043576731287 chr6 171115067 14932195 0.08726405723231842 0.38220552808732566 chr7 159138663 14204647 0.08925955975890032 0.7268541782341094 chr8 146364022 13293412 0.09082431473494217 3.4285501554431113 chr9 141213431 10749100 0.07611953001835924 0.44571979031629294 chr10 135534747 11870238 0.08758077365946608 0.4455698591569691 chr11 135006516 11531440 0.08541395142735185 0.5160994174834945 chr12 133851895 11612637 0.08675735969221803 0.35588964850326715 chr13 115169878 8363029 0.07261472483282477 0.31127016295079396 chr14 107349540 7881293 0.073417110124552 0.36745103489830927 chr15 102531392 7313652 0.07133085640737229 0.3096680277624557 chr16 90354753 7098335 0.07856072607491937 0.35533242965065 chr17 81195210 6743853 0.08305727640830043 0.36197834556979985 chr18 78077248 6782873 0.08687387393572069 0.8115553388920018 chr19 59128983 5016647 0.08484243674544513 0.7853206101182728 chr20 63025520 5151223 0.08173233636152466 0.3406356431197204 chr21 48129895 3250180 0.06752933909371711 0.3390368698045934 chr22 51304566 2809171 0.054754795119015334 0.3219739430710287 chrMT 16571 11038 0.6661034337094924 0.9974183771862195 chrX 155270560 14782149 0.09520252261600654 0.4261921895451228 chrY 59373566 779608 0.013130557123686996 0.1831148985766255