BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081147.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 = 2,811,145 number of mapped reads = 2,529,250 (89.97%) number of supplementary alignments = 23,976 (0.85%) number of secondary alignments = 0 number of mapped bases = 170,798,536 bp number of sequenced bases = 170,735,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,862 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2989 >>>>>>> ACTG content number of A's = 49,056,680 bp (28.73%) number of C's = 31,549,105 bp (18.48%) number of T's = 53,630,624 bp (31.41%) number of G's = 36,447,751 bp (21.35%) number of N's = 51,214 bp (0.03%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,395,708 number of insertions = 13,459 mapped reads with insertion percentage = 0.53% number of deletions = 38,912 mapped reads with deletion percentage = 1.52% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0552X std coverageData = 0.4041X There is a 4.68% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% 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 13190195 0.052919406768499086 0.6811918992962648 chr2 243199373 14627510 0.0601461665774936 0.4689143645929426 chr3 198022430 11818930 0.0596848043931185 0.2758972719518204 chr4 191154276 11769179 0.06156900722430086 0.2922591552395064 chr5 180915260 10871256 0.060090320739112885 0.2794010206822553 chr6 171115067 10328440 0.06035961754320559 0.390788013781909 chr7 159138663 8867906 0.05572439677968138 0.49045341590052094 chr8 146364022 8958404 0.06120632569115927 0.5828823307941118 chr9 141213431 7448550 0.05274675324615546 0.3744087276134721 chr10 135534747 7768060 0.057314158707951104 0.36467232861627025 chr11 135006516 7701744 0.05704720207726863 0.3657757754551642 chr12 133851895 7741915 0.057839412733006135 0.2782355838774184 chr13 115169878 5846740 0.05076622552296183 0.2559206838240174 chr14 107349540 5040834 0.046957201679671844 0.26113342289772107 chr15 102531392 4692516 0.04576662725889843 0.24487578443404795 chr16 90354753 4650793 0.05147258827656803 0.2861194285415327 chr17 81195210 4371825 0.05384338558887895 0.30694736531213185 chr18 78077248 4697659 0.06016681069496712 0.6491881287609967 chr19 59128983 2762509 0.04672004928615126 0.4972480406531099 chr20 63025520 3274988 0.05196288741449495 0.26701660994753507 chr21 48129895 2273428 0.0472352578371509 0.2666427992287733 chr22 51304566 1734445 0.03380683504856079 0.20595954562799965 chrMT 16571 1365 0.0823728199867238 0.28433715215899524 chrX 155270560 9955774 0.06411887739697725 0.31471140828191385 chrY 59373566 403571 0.006797149425048851 0.1352090573014877