BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819060.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 = 3,325,019 number of mapped reads = 3,001,248 (90.26%) number of supplementary alignments = 13,246 (0.4%) number of secondary alignments = 0 number of mapped bases = 173,443,628 bp number of sequenced bases = 173,399,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,169 duplication rate = 3.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8832 >>>>>>> ACTG content number of A's = 44,292,532 bp (25.54%) number of C's = 33,350,330 bp (19.23%) number of T's = 54,568,215 bp (31.47%) number of G's = 41,184,495 bp (23.75%) number of N's = 4,055 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 825,019 number of insertions = 9,830 mapped reads with insertion percentage = 0.33% number of deletions = 26,392 mapped reads with deletion percentage = 0.87% homopolymer indels = 41.71% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.3797X There is a 4.69% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.13% 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 0.01% 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 18959016 0.07606406725863282 0.6083135110259199 chr2 243199373 14237281 0.058541602407831864 0.44287917835972984 chr3 198022430 11226700 0.05669408258448298 0.2758805017104034 chr4 191154276 10804996 0.05652500287254887 0.30340648030160383 chr5 180915260 8440968 0.04665702605739284 0.2580374190885877 chr6 171115067 8995792 0.05257159499578141 0.29379826906920153 chr7 159138663 7264319 0.04564773175202559 0.32629411106168144 chr8 146364022 14634039 0.09998385395558479 0.459840044947444 chr9 141213431 6206461 0.043950925602820316 0.38959758494444274 chr10 135534747 7981582 0.05888956283660603 0.3715952999107597 chr11 135006516 5322744 0.039425830379920326 0.35906314825109653 chr12 133851895 7660889 0.05723407203162869 0.2869841682671049 chr13 115169878 5314011 0.04614063236222235 0.2473503720043642 chr14 107349540 6014910 0.05603107381736335 0.30649601758733663 chr15 102531392 4877823 0.047573946913741304 0.25457733308090447 chr16 90354753 4904780 0.054283585944836794 0.30196452222966347 chr17 81195210 3720029 0.04581586770943754 0.26628760078278463 chr18 78077248 4163130 0.05332065494931379 0.7622348367191776 chr19 59128983 3130419 0.05294220940684875 0.46411580895353755 chr20 63025520 5421661 0.08602326486159892 0.35601747642760256 chr21 48129895 2168508 0.04505532372343634 0.27642195185862706 chr22 51304566 2000268 0.03898810877768657 0.22686919860287638 chrMT 16571 8492 0.5124615291774788 0.8854569144107852 chrX 155270560 9534189 0.0614037136209208 0.3402563740441894 chrY 59373566 450621 0.007589589616362271 0.15567170465872296