BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063558.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 = 3,663,310 number of mapped reads = 3,146,888 (85.9%) number of supplementary alignments = 30,718 (0.84%) number of secondary alignments = 0 number of mapped bases = 201,633,283 bp number of sequenced bases = 201,543,707 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,661 duplication rate = 6.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1565 >>>>>>> ACTG content number of A's = 54,238,133 bp (26.91%) number of C's = 36,608,576 bp (18.16%) number of T's = 64,418,008 bp (31.96%) number of G's = 46,274,037 bp (22.96%) number of N's = 4,953 bp (0%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,707,391 number of insertions = 14,835 mapped reads with insertion percentage = 0.47% number of deletions = 55,943 mapped reads with deletion percentage = 1.76% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0651X std coverageData = 0.6251X There is a 4.93% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 19391755 0.07780022742651461 1.1660982518503127 chr2 243199373 19334591 0.07950099032533278 0.9775716446796153 chr3 198022430 13045203 0.06587740085807452 0.32487215850789347 chr4 191154276 12311305 0.06440507247664184 0.3498315009257239 chr5 180915260 10321787 0.05705315847872645 0.3039034632865073 chr6 171115067 14263021 0.08335339049950523 0.447429200914415 chr7 159138663 15760606 0.09903693862251438 1.0071065780349149 chr8 146364022 7941768 0.054260383743759105 0.7449875875596947 chr9 141213431 5355022 0.03792147787982009 0.4674073878467742 chr10 135534747 9327779 0.06882204900563248 0.4296406331588547 chr11 135006516 11188507 0.0828738295861216 0.5452186506339955 chr12 133851895 8662258 0.064715243665396 0.3440227562015649 chr13 115169878 4956643 0.0430376682347445 0.27627523362731216 chr14 107349540 3902182 0.036350244258149596 0.3142516664471525 chr15 102531392 3758801 0.03666000165100655 0.264734281671099 chr16 90354753 4347234 0.04811295317248004 0.3118347444587516 chr17 81195210 6205208 0.07642332595728246 0.40337684205821506 chr18 78077248 5614613 0.0719110002442709 0.8075443635211318 chr19 59128983 4660731 0.07882312131091448 0.8393220752878261 chr20 63025520 2392984 0.037968492762931585 0.27256536246641316 chr21 48129895 3768500 0.0782985294275003 0.3739659533857077 chr22 51304566 2392536 0.04663397795821916 0.268205508236468 chrMT 16571 52371 3.160400700018104 2.716941778037593 chrX 155270560 12201553 0.07858252717063685 0.43541145511435947 chrY 59373566 476325 0.008022509545746334 0.16134997478791097