BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013352.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 = 2,604,791 number of mapped reads = 2,372,730 (91.09%) number of supplementary alignments = 22,863 (0.88%) number of secondary alignments = 0 number of mapped bases = 156,930,699 bp number of sequenced bases = 156,866,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 153,007 duplication rate = 5.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6728 >>>>>>> ACTG content number of A's = 42,919,550 bp (27.36%) number of C's = 29,365,217 bp (18.72%) number of T's = 49,331,393 bp (31.45%) number of G's = 35,232,750 bp (22.46%) number of N's = 17,241 bp (0.01%) GC percentage = 41.18% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,147,979 number of insertions = 11,801 mapped reads with insertion percentage = 0.49% number of deletions = 36,885 mapped reads with deletion percentage = 1.54% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0507X std coverageData = 0.4597X There is a 3.74% of reference with a coverageData >= 1X There is a 0.9% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% 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 12546752 0.05033789665061657 0.8918410866730483 chr2 243199373 13520544 0.05559448543479592 0.5570382739035427 chr3 198022430 10424080 0.052640905376224296 0.29721786195641314 chr4 191154276 9753158 0.05102244220788448 0.31782075225660056 chr5 180915260 9599336 0.05305984691396403 0.297550434162632 chr6 171115067 9132167 0.05336857332382075 0.3643632606989383 chr7 159138663 8409177 0.05284182260598733 0.5909264330686296 chr8 146364022 7991201 0.05459812384767617 0.45118284948518833 chr9 141213431 6471951 0.04583098756378209 0.36183574630981447 chr10 135534747 7558445 0.0557675811354855 0.4983476685324013 chr11 135006516 7031280 0.05208104177727244 0.35825029639366107 chr12 133851895 7015676 0.052413721897624235 0.2982992817289776 chr13 115169878 4873089 0.04231218339920444 0.26599132722784335 chr14 107349540 4660888 0.04341786653207829 0.2828819720243364 chr15 102531392 4427362 0.043180550986765105 0.2691299872804822 chr16 90354753 4414363 0.04885590246702351 0.322717257249757 chr17 81195210 4423834 0.05448392830069656 0.3246343175154371 chr18 78077248 4219673 0.05404484799464243 0.6662542496930494 chr19 59128983 3404997 0.05758592194964693 0.6119903640824508 chr20 63025520 3106589 0.04929096975320473 0.2918771216926076 chr21 48129895 2129813 0.04425135355063625 0.2954199250114288 chr22 51304566 1759639 0.03429790245180127 0.23738543829511272 chrMT 16571 299006 18.043932170659588 10.614759931000988 chrX 155270560 9332019 0.06010166383118603 0.33760874235005744 chrY 59373566 425660 0.007169183673421267 0.1744021894864175