BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084893.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 = 2,307,774 number of mapped reads = 2,064,768 (89.47%) number of supplementary alignments = 15,879 (0.69%) number of secondary alignments = 0 number of mapped bases = 139,852,540 bp number of sequenced bases = 139,801,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,782 duplication rate = 4.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3342 >>>>>>> ACTG content number of A's = 39,712,471 bp (28.41%) number of C's = 25,197,827 bp (18.02%) number of T's = 45,108,773 bp (32.27%) number of G's = 29,760,713 bp (21.29%) number of N's = 21,625 bp (0.02%) GC percentage = 39.31% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,117,839 number of insertions = 10,592 mapped reads with insertion percentage = 0.51% number of deletions = 29,574 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.82% >>>>>>> Coverage mean coverageData = 0.0452X std coverageData = 0.3138X There is a 3.82% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 11118657 0.04460834221953654 0.4651229437497401 chr2 243199373 12765565 0.05249012299057202 0.4019364902785321 chr3 198022430 10509983 0.0530747097689893 0.2640209551350561 chr4 191154276 8692983 0.045476267556787485 0.24466939302510787 chr5 180915260 8087327 0.044702293217277526 0.24303815418341698 chr6 171115067 8009727 0.046809010687527595 0.2540246360534717 chr7 159138663 7086347 0.04452938630004702 0.2967487102418244 chr8 146364022 7714777 0.05270951764361873 0.41802573956336186 chr9 141213431 9083364 0.06432365487954188 0.3884662028195888 chr10 135534747 4241224 0.03129252161440195 0.22761560629506553 chr11 135006516 6410520 0.04748304148519765 0.30419375862361886 chr12 133851895 5855944 0.04374942917319176 0.2432678800278648 chr13 115169878 4263502 0.037019245605174646 0.2185097649041275 chr14 107349540 2843593 0.02648910279447867 0.19216122744201564 chr15 102531392 3615265 0.035260079176531615 0.21378296809380265 chr16 90354753 2831961 0.03134268985274079 0.21444549234898827 chr17 81195210 3189023 0.03927599916300481 0.2326178520825465 chr18 78077248 5959708 0.0763309178110376 0.5535845826912704 chr19 59128983 2567188 0.04341674538863623 0.33099111194581976 chr20 63025520 2860965 0.045393754783776476 0.24803207051473408 chr21 48129895 1254077 0.026056092580297546 0.1939915080208665 chr22 51304566 1239379 0.024157284558259395 0.17475661090866956 chrMT 16571 110241 6.652646189125581 3.9562767785768282 chrX 155270560 9240781 0.059514057268808714 0.29658228497299693 chrY 59373566 300439 0.005060147473709091 0.12556499239961227