BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779293.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 14,305,734 number of mapped reads = 13,772,663 (96.27%) number of supplementary alignments = 38,333 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,926,099 number of mapped paired reads (second in pair) = 6,846,564 number of mapped paired reads (both in pair) = 13,672,514 number of mapped paired reads (singletons) = 100,149 number of mapped bases = 1,096,048,211 bp number of sequenced bases = 1,095,844,345 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 189,600 duplication rate = 1.28% >>>>>>> Insert size mean insert size = 61,462.5763 std insert size = 2,315,468.7679 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 52.9136 >>>>>>> ACTG content number of A's = 333,995,052 bp (30.48%) number of C's = 213,680,929 bp (19.5%) number of T's = 329,894,072 bp (30.1%) number of G's = 218,066,086 bp (19.9%) number of N's = 208,206 bp (0.02%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 4,089,577 number of insertions = 77,921 mapped reads with insertion percentage = 0.56% number of deletions = 98,771 mapped reads with deletion percentage = 0.71% homopolymer indels = 46.39% >>>>>>> Coverage mean coverageData = 0.3541X std coverageData = 0.9635X There is a 21.18% of reference with a coverageData >= 1X There is a 7.86% of reference with a coverageData >= 2X There is a 3.16% of reference with a coverageData >= 3X There is a 1.41% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 88619825 0.355545051982037 1.0142506406609042 chr2 243199373 69163416 0.28438977924503117 0.7438273509091616 chr3 198022430 77972970 0.39375827273708336 0.9002312041220484 chr4 191154276 67170219 0.35139270962476404 0.8393975052519247 chr5 180915260 36113303 0.19961446591072526 0.6035651266112546 chr6 171115067 71077897 0.41538070402648997 0.9297264168149895 chr7 159138663 113338333 0.7121986000347382 1.9832841099914398 chr8 146364022 83035914 0.5673246257198371 1.1031340273534107 chr9 141213431 51466712 0.36446045985526687 0.911737247491502 chr10 135534747 36450449 0.26893803845002195 1.0143002299572936 chr11 135006516 66753406 0.4944458088230349 1.0268137749775963 chr12 133851895 25245998 0.18861143504916386 0.5993279717376375 chr13 115169878 33424564 0.2902196701120062 0.7676301000328585 chr14 107349540 43020036 0.40074727846994035 0.9249792451075687 chr15 102531392 41042313 0.4002902155078515 0.9720532631735389 chr16 90354753 24466005 0.2707771775990578 0.7132810510779072 chr17 81195210 28674463 0.35315461343101395 0.8649664830583573 chr18 78077248 20771798 0.2660416258523866 0.7110490803305184 chr19 59128983 15116756 0.2556572975388398 0.7830859506466822 chr20 63025520 29516638 0.46832835334004386 1.090332282500716 chr21 48129895 12843775 0.2668564932460376 0.7338988000266305 chr22 51304566 7975825 0.1554603346610514 0.5434378929977448 chrMT 16571 187 0.011284774606239816 0.12595414543905184 chrX 155270560 52113985 0.33563339373542544 0.8485057442989392 chrY 59373566 673424 0.01134215182561209 0.17118956627117332