BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238310.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 = 2,557,575 number of mapped reads = 2,184,399 (85.41%) number of supplementary alignments = 30,335 (1.19%) number of secondary alignments = 0 number of mapped bases = 139,301,186 bp number of sequenced bases = 139,215,837 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 154,627 duplication rate = 5.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0119 >>>>>>> ACTG content number of A's = 38,856,428 bp (27.91%) number of C's = 26,683,752 bp (19.17%) number of T's = 42,811,812 bp (30.75%) number of G's = 30,827,316 bp (22.14%) number of N's = 36,529 bp (0.03%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,300,770 number of insertions = 10,951 mapped reads with insertion percentage = 0.5% number of deletions = 51,172 mapped reads with deletion percentage = 2.31% homopolymer indels = 44.25% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.392X There is a 3.33% of reference with a coverageData >= 1X There is a 0.8% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 10895575 0.04371333141031573 0.6445610584503964 chr2 243199373 10767465 0.04427423009844684 0.47956413750536503 chr3 198022430 10888419 0.054985786206138365 0.3029543299013164 chr4 191154276 9812311 0.05133189382590636 0.3058549897668237 chr5 180915260 8777947 0.04851966053057105 0.2856309070077554 chr6 171115067 6335501 0.037024799224722856 0.27141639844610355 chr7 159138663 7022273 0.04412675629931615 0.3727088072964351 chr8 146364022 6624004 0.045257050943844655 0.6100572238771714 chr9 141213431 5425222 0.03841859773239275 0.3478233818336541 chr10 135534747 9397187 0.069334153846172 0.4285014093475367 chr11 135006516 6510562 0.04822405757067311 0.3481875696215498 chr12 133851895 6748303 0.05041619321116074 0.29611790167819146 chr13 115169878 4928922 0.0427969716178739 0.2703186742618032 chr14 107349540 4639056 0.043214493513432845 0.3052441660687179 chr15 102531392 4343877 0.04236631255333001 0.2955802762160651 chr16 90354753 3593008 0.0397655671749775 0.27929508445506185 chr17 81195210 3118132 0.03840290578717636 0.2772512940407991 chr18 78077248 3407244 0.043639396716441646 0.5643693976618244 chr19 59128983 3378969 0.057145731730241324 0.5121199092098645 chr20 63025520 3051511 0.048417069783795515 0.29462289926016744 chr21 48129895 2081426 0.04324601165242517 0.2827610967115744 chr22 51304566 1712806 0.03338505972353416 0.2343975529095811 chrMT 16571 6790 0.4097519763442158 0.8092586298811213 chrX 155270560 5523601 0.0355740392769885 0.2699791445862162 chrY 59373566 311075 0.005239284431728422 0.15127360544196722