BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672006.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 214,042,306 number of mapped reads = 213,039,048 (99.53%) number of supplementary alignments = 915,311 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 106,529,212 number of mapped paired reads (second in pair) = 106,509,836 number of mapped paired reads (both in pair) = 212,672,012 number of mapped paired reads (singletons) = 367,036 number of mapped bases = 31,595,416,197 bp number of sequenced bases = 31,582,523,913 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,971,157 duplication rate = 24.1% >>>>>>> Insert size mean insert size = 64,150.9896 std insert size = 2,438,779.8203 median insert size = 364 >>>>>>> Mapping quality mean mapping quality = 54.5518 >>>>>>> ACTG content number of A's = 9,207,219,293 bp (29.15%) number of C's = 6,595,244,945 bp (20.88%) number of T's = 9,158,870,078 bp (29%) number of G's = 6,621,053,015 bp (20.96%) number of N's = 136,582 bp (0%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 181,493,130 number of insertions = 4,374,085 mapped reads with insertion percentage = 1.95% number of deletions = 4,649,166 mapped reads with deletion percentage = 2.1% homopolymer indels = 46.1% >>>>>>> Coverage mean coverageData = 10.2062X std coverageData = 106.5898X There is a 92.09% of reference with a coverageData >= 1X There is a 91.46% of reference with a coverageData >= 2X There is a 90.18% of reference with a coverageData >= 3X There is a 88% of reference with a coverageData >= 4X There is a 84.68% of reference with a coverageData >= 5X There is a 80.07% of reference with a coverageData >= 6X There is a 74.2% of reference with a coverageData >= 7X There is a 67.22% of reference with a coverageData >= 8X There is a 59.43% of reference with a coverageData >= 9X There is a 51.24% of reference with a coverageData >= 10X There is a 43.09% of reference with a coverageData >= 11X There is a 35.36% of reference with a coverageData >= 12X There is a 28.33% of reference with a coverageData >= 13X There is a 22.2% of reference with a coverageData >= 14X There is a 17.03% of reference with a coverageData >= 15X There is a 12.83% of reference with a coverageData >= 16X There is a 9.5% of reference with a coverageData >= 17X There is a 6.95% of reference with a coverageData >= 18X There is a 5.03% of reference with a coverageData >= 19X There is a 3.62% of reference with a coverageData >= 20X There is a 2.6% of reference with a coverageData >= 21X There is a 1.88% of reference with a coverageData >= 22X There is a 1.38% of reference with a coverageData >= 23X There is a 1.03% of reference with a coverageData >= 24X There is a 0.79% of reference with a coverageData >= 25X There is a 0.62% of reference with a coverageData >= 26X There is a 0.51% of reference with a coverageData >= 27X There is a 0.43% of reference with a coverageData >= 28X There is a 0.37% of reference with a coverageData >= 29X There is a 0.33% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.28% of reference with a coverageData >= 32X There is a 0.26% of reference with a coverageData >= 33X There is a 0.24% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.21% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2648740442 10.626815818444841 282.63453788084297 chr2 243199373 2714234777 11.160533612888878 63.63524903862338 chr3 198022430 2082696900 10.517479762267335 7.448588543292875 chr4 191154276 2040385338 10.674024043281145 62.88763843955699 chr5 180915260 1893034474 10.46365283945644 9.137663610440619 chr6 171115067 1819126727 10.631014316232012 49.177513068127936 chr7 159138663 1732619780 10.88748483453075 74.56995425940177 chr8 146364022 1580647759 10.79942828436349 56.51688757975121 chr9 141213431 1402289690 9.930285526452508 179.68505523199664 chr10 135534747 1592836604 11.752237999898284 132.6882300260533 chr11 135006516 1467928868 10.87302236582418 45.52018418577453 chr12 133851895 1413128238 10.557401805928858 8.569515326820431 chr13 115169878 995268797 8.641745691525347 6.480973147819076 chr14 107349540 963163394 8.972217244712926 8.039698902863163 chr15 102531392 910752428 8.882669104892285 6.454279844111291 chr16 90354753 1048182392 11.6007443681463 63.516232130220025 chr17 81195210 944868319 11.636995815393544 55.838324263618176 chr18 78077248 910166027 11.657250355442855 172.56451144990373 chr19 59128983 696491012 11.779181319590766 117.81651066277487 chr20 63025520 696089826 11.044570929363216 25.032282810167764 chr21 48129895 452708299 9.405968972091047 40.42105974968026 chr22 51304566 439125317 8.559185882207833 39.80013998487792 chrMT 16571 16539746 998.1139339810512 115.80453165832093 chrX 155270560 829175186 5.340195758938462 15.58785452256195 chrY 59373566 305215857 5.140601745227834 87.22922718282173