BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525149.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,422,228 number of mapped reads = 1,345,935 (94.64%) number of supplementary alignments = 5,976 (0.42%) number of secondary alignments = 0 number of mapped bases = 84,013,708 bp number of sequenced bases = 83,987,732 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,155 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1507 >>>>>>> ACTG content number of A's = 22,893,803 bp (27.26%) number of C's = 18,421,277 bp (21.93%) number of T's = 23,820,349 bp (28.36%) number of G's = 18,850,116 bp (22.44%) number of N's = 2,187 bp (0%) GC percentage = 44.38% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 383,333 number of insertions = 5,450 mapped reads with insertion percentage = 0.4% number of deletions = 15,932 mapped reads with deletion percentage = 1.17% homopolymer indels = 44.17% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.2582X There is a 2.46% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 8329743 0.03341914642611863 0.47668995317013985 chr2 243199373 6992380 0.028751636625313173 0.2788883920137754 chr3 198022430 6327482 0.03195336003098235 0.19088889273170692 chr4 191154276 4502868 0.02355619813600194 0.17330865619668934 chr5 180915260 3811289 0.021066708247828293 0.15531230675741722 chr6 171115067 5421571 0.03168377335234892 0.20782289574906526 chr7 159138663 6211345 0.039031024157844034 0.4103089926736846 chr8 146364022 4380261 0.029927170216735365 0.22643674018423604 chr9 141213431 2867307 0.020304775400577867 0.20127848231056572 chr10 135534747 4090761 0.0301823782502062 0.2493755218311126 chr11 135006516 3958677 0.029322118052435335 0.2144426812514647 chr12 133851895 3851554 0.02877474390631526 0.18406346043144656 chr13 115169878 1977173 0.017167448940077892 0.14036116549765873 chr14 107349540 3963830 0.03692451779485967 0.21554740265831857 chr15 102531392 1603929 0.015643296835373112 0.13478674547406755 chr16 90354753 2179248 0.02411879760215824 0.18235149477692134 chr17 81195210 1611290 0.019844643544859358 0.15913591441725652 chr18 78077248 1775163 0.02273598321498217 0.3679075266534739 chr19 59128983 1607774 0.027190963186361584 0.3378552068647108 chr20 63025520 1642020 0.026053255887456384 0.17472863314308848 chr21 48129895 1125716 0.023389122290834 0.17522085743636423 chr22 51304566 745261 0.014526211955481701 0.12834860797731804 chrMT 16571 232638 14.038863074045018 7.497985450624243 chrX 155270560 4569207 0.029427387909208288 0.1950263628374919 chrY 59373566 235221 0.003961712523718046 0.12385702324405934