BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068130.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 = 4,051,642 number of mapped reads = 3,781,282 (93.33%) number of supplementary alignments = 21,570 (0.53%) number of secondary alignments = 0 number of mapped bases = 237,756,281 bp number of sequenced bases = 237,633,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 834,228 duplication rate = 17.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7503 >>>>>>> ACTG content number of A's = 60,683,503 bp (25.54%) number of C's = 41,170,788 bp (17.33%) number of T's = 79,387,179 bp (33.41%) number of G's = 56,367,281 bp (23.72%) number of N's = 25,209 bp (0.01%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,462,703 number of insertions = 15,156 mapped reads with insertion percentage = 0.4% number of deletions = 69,275 mapped reads with deletion percentage = 1.81% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.0768X std coverageData = 0.7571X There is a 4.29% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.17% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% 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 24243812 0.09726680680968093 1.5360282295204963 chr2 243199373 22141970 0.0910445192636249 1.0842175736679418 chr3 198022430 15986669 0.08073160702047742 0.4579410934175025 chr4 191154276 12705276 0.06646608313381386 0.4349819629257132 chr5 180915260 11208759 0.06195585159593502 0.40441264015610084 chr6 171115067 13759031 0.08040806248815015 0.5375418804619709 chr7 159138663 21622189 0.13587011850162395 1.14004833508343 chr8 146364022 9100585 0.062177746113044094 0.8012804631777035 chr9 141213431 9199615 0.06514688393910634 0.5715652074020723 chr10 135534747 11704304 0.08635648244505152 0.571226934858333 chr11 135006516 12049814 0.08925357350900011 0.6006765501883585 chr12 133851895 9654640 0.07212927392623018 0.4496189815033951 chr13 115169878 5243339 0.045526999689971016 0.36076895359816674 chr14 107349540 5316579 0.049525866622251016 0.38528290121995684 chr15 102531392 4791332 0.04673039063002285 0.38627382687288336 chr16 90354753 4997372 0.055308346645582665 0.40455922649392195 chr17 81195210 6061152 0.074649132627405 0.47101173723267775 chr18 78077248 6310032 0.08081780751288775 0.8803828782456918 chr19 59128983 4614465 0.0780406623939397 0.8954002699858541 chr20 63025520 3602249 0.05715540308116458 0.40624102204994766 chr21 48129895 4110950 0.08541364987395049 0.4812427740757082 chr22 51304566 2600774 0.05069283696893567 0.3575076489148142 chrMT 16571 176387 10.644318387544505 8.104961032673309 chrX 155270560 15855736 0.10211682111534859 0.5880677891514677 chrY 59373566 699250 0.011777126541464598 0.2397109891983984