BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082916.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 = 2,225,566 number of mapped reads = 1,992,364 (89.52%) number of supplementary alignments = 17,393 (0.78%) number of secondary alignments = 0 number of mapped bases = 131,815,647 bp number of sequenced bases = 131,765,063 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,303 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7312 >>>>>>> ACTG content number of A's = 35,131,867 bp (26.66%) number of C's = 24,694,725 bp (18.74%) number of T's = 41,388,023 bp (31.41%) number of G's = 30,544,177 bp (23.18%) number of N's = 6,271 bp (0%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 969,189 number of insertions = 10,562 mapped reads with insertion percentage = 0.53% number of deletions = 30,972 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 0.3358X There is a 3.5% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 11708302 0.046974013356620686 0.38915893336629276 chr2 243199373 13289893 0.05464608249627354 0.5767635962130064 chr3 198022430 8557913 0.04321688709708289 0.24228902693075632 chr4 191154276 8448815 0.04419893280336559 0.25486868799669643 chr5 180915260 7141836 0.039476139270949284 0.23371428544754708 chr6 171115067 8624160 0.050399769881164236 0.34205782792438705 chr7 159138663 7157834 0.044978598318373454 0.3421675083012711 chr8 146364022 12016888 0.08210274516779814 0.42658064315079214 chr9 141213431 4041749 0.028621562208201005 0.30612299653312125 chr10 135534747 4231423 0.03122020805483925 0.2441520204323156 chr11 135006516 5129204 0.03799226994347443 0.3064706100806563 chr12 133851895 4099102 0.030624161129732232 0.20752025830948884 chr13 115169878 2435852 0.021150078842664052 0.17376919153919201 chr14 107349540 3085458 0.028742163217466976 0.21281999777666183 chr15 102531392 2592625 0.025286158213866834 0.2109515043707943 chr16 90354753 7525604 0.08328951992154746 0.3599027465295571 chr17 81195210 3717757 0.0457878857632119 0.27538840074036686 chr18 78077248 4551129 0.05829007958887075 0.6505951415534199 chr19 59128983 1117952 0.018907005385159423 0.3119618748442968 chr20 63025520 2679170 0.042509288300992994 0.25051395834605567 chr21 48129895 2799781 0.05817135067508458 0.2902376982729263 chr22 51304566 1842496 0.035912904905968795 0.2202397237793718 chrMT 16571 133938 8.082674551928067 5.4546928706717805 chrX 155270560 4644473 0.029912128867185125 0.23403246562451513 chrY 59373566 242293 0.004080822768839588 0.08834877755895576