BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818878.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,470,463 number of mapped reads = 1,447,290 (98.42%) number of supplementary alignments = 22,907 (1.56%) number of secondary alignments = 0 number of mapped bases = 133,948,062 bp number of sequenced bases = 133,868,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 179,241 duplication rate = 9.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1926 >>>>>>> ACTG content number of A's = 38,040,708 bp (28.42%) number of C's = 29,367,195 bp (21.94%) number of T's = 37,332,451 bp (27.89%) number of G's = 29,125,928 bp (21.76%) number of N's = 1,968 bp (0%) GC percentage = 43.69% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 808,696 number of insertions = 18,511 mapped reads with insertion percentage = 1.24% number of deletions = 38,738 mapped reads with deletion percentage = 2.62% homopolymer indels = 40.64% >>>>>>> Coverage mean coverageData = 0.0433X std coverageData = 0.5781X There is a 3.44% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 12768228 0.05122646414590076 0.8478105097417065 chr2 243199373 10071844 0.04141393900715361 0.6823097153673865 chr3 198022430 8063220 0.04071872060149954 0.24539120914411786 chr4 191154276 6652755 0.034803066607832514 0.3707845107250396 chr5 180915260 5816793 0.03215203073527352 0.21954666205170634 chr6 171115067 6478289 0.03785925525775004 0.26236343559454994 chr7 159138663 11917727 0.07488894763430305 1.3302060441726309 chr8 146364022 11347229 0.07752744728482523 0.46340654956444427 chr9 141213431 4922424 0.03485804406239517 0.5039480188977055 chr10 135534747 6596009 0.048666553382063715 0.9905502735252937 chr11 135006516 5888329 0.043615146694104746 0.32957436126119355 chr12 133851895 5198154 0.03883511697761171 0.233532279776796 chr13 115169878 3952290 0.03431704599009821 0.21666892554509024 chr14 107349540 3874145 0.03608906940821544 0.24898717053768774 chr15 102531392 3724641 0.036326835394958845 0.22539265030009822 chr16 90354753 3547008 0.039256462800578956 0.45794651082853366 chr17 81195210 3533956 0.043524193114347506 0.4181810469254351 chr18 78077248 2575916 0.03299189028793638 0.6032985287641149 chr19 59128983 2557235 0.04324841846172122 0.7918439513106567 chr20 63025520 5740853 0.09108775302448913 0.39266589288925663 chr21 48129895 1327706 0.0275858902247761 0.2722403221787094 chr22 51304566 1302118 0.025380158171496862 0.2010606034257748 chrMT 16571 161336 9.736044897712873 6.914180452920411 chrX 155270560 5326008 0.034301467064973556 0.2995764421482699 chrY 59373566 603849 0.010170334050678378 0.728114432325662