BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068179.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,674,547 number of mapped reads = 4,403,838 (94.21%) number of supplementary alignments = 36,881 (0.79%) number of secondary alignments = 0 number of mapped bases = 280,693,877 bp number of sequenced bases = 280,573,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 562,128 duplication rate = 10.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5045 >>>>>>> ACTG content number of A's = 72,798,306 bp (25.95%) number of C's = 50,302,877 bp (17.93%) number of T's = 91,567,894 bp (32.64%) number of G's = 65,874,386 bp (23.48%) number of N's = 30,434 bp (0.01%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,621,477 number of insertions = 17,267 mapped reads with insertion percentage = 0.39% number of deletions = 68,373 mapped reads with deletion percentage = 1.54% homopolymer indels = 44.15% >>>>>>> Coverage mean coverageData = 0.0907X std coverageData = 0.8533X There is a 6.53% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% 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 28615694 0.11480691155429458 1.7527932581084085 chr2 243199373 27300029 0.11225369812117073 1.3238951643788164 chr3 198022430 13011080 0.0657050819950043 0.3417794781470269 chr4 191154276 14861792 0.07774763040090193 0.39454671307303846 chr5 180915260 13151819 0.07269601801417967 0.35761518787590213 chr6 171115067 15403286 0.09001712280543946 0.5380782952651895 chr7 159138663 24375198 0.15316955377462232 1.4925755072640918 chr8 146364022 11243534 0.07681897399621883 0.7844701265056079 chr9 141213431 8670392 0.061399202176455864 0.5188541673325359 chr10 135534747 16071369 0.11857748183202053 0.6532310826364026 chr11 135006516 15007560 0.11116174570418512 0.5427586057568333 chr12 133851895 10320403 0.07710315195761704 0.3870917504510897 chr13 115169878 7494526 0.06507366448716738 0.36877732831958515 chr14 107349540 6014998 0.05603189356936229 0.353036342200395 chr15 102531392 6175213 0.06022753499728161 0.36254739400285946 chr16 90354753 6537924 0.07235838495402672 0.3857486659683904 chr17 81195210 8831435 0.10876793101464975 0.4764302208083175 chr18 78077248 8085902 0.10356284586260008 1.0711261641550283 chr19 59128983 6299930 0.10654554975180276 1.1956929452256877 chr20 63025520 4919377 0.0780537312504522 0.4010585912691375 chr21 48129895 4994357 0.10376829203554257 0.44292343056478295 chr22 51304566 3409323 0.06645262333960684 0.335264024712781 chrMT 16571 71826 4.334439683784925 3.3584994880570553 chrX 155270560 18992391 0.12231804277642845 0.566321142557628 chrY 59373566 834519 0.01405539630211869 0.40428839375476605