BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779338.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 132,261,130 number of mapped reads = 126,674,809 (95.78%) number of supplementary alignments = 458,681 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 64,024,028 number of mapped paired reads (second in pair) = 62,650,781 number of mapped paired reads (both in pair) = 124,414,210 number of mapped paired reads (singletons) = 2,260,599 number of mapped bases = 12,547,201,694 bp number of sequenced bases = 12,544,257,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,577,368 duplication rate = 5.66% >>>>>>> Insert size mean insert size = 53,372.0829 std insert size = 2,302,924.6044 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 53.8985 >>>>>>> ACTG content number of A's = 3,737,878,682 bp (29.8%) number of C's = 2,521,842,829 bp (20.1%) number of T's = 3,719,724,122 bp (29.65%) number of G's = 2,564,151,754 bp (20.44%) number of N's = 660,294 bp (0.01%) GC percentage = 40.54% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 49,523,573 number of insertions = 1,330,120 mapped reads with insertion percentage = 1.03% number of deletions = 1,330,764 mapped reads with deletion percentage = 1.03% homopolymer indels = 48.02% >>>>>>> Coverage mean coverageData = 4.0531X std coverageData = 7.9954X There is a 80.41% of reference with a coverageData >= 1X There is a 67.13% of reference with a coverageData >= 2X There is a 54.13% of reference with a coverageData >= 3X There is a 42.8% of reference with a coverageData >= 4X There is a 33.49% of reference with a coverageData >= 5X There is a 26.08% of reference with a coverageData >= 6X There is a 20.3% of reference with a coverageData >= 7X There is a 15.83% of reference with a coverageData >= 8X There is a 12.39% of reference with a coverageData >= 9X There is a 9.73% of reference with a coverageData >= 10X There is a 7.69% of reference with a coverageData >= 11X There is a 6.1% of reference with a coverageData >= 12X There is a 4.87% of reference with a coverageData >= 13X There is a 3.91% of reference with a coverageData >= 14X There is a 3.15% of reference with a coverageData >= 15X There is a 2.56% of reference with a coverageData >= 16X There is a 2.09% of reference with a coverageData >= 17X There is a 1.71% of reference with a coverageData >= 18X There is a 1.41% of reference with a coverageData >= 19X There is a 1.17% of reference with a coverageData >= 20X There is a 0.98% of reference with a coverageData >= 21X There is a 0.82% of reference with a coverageData >= 22X There is a 0.69% of reference with a coverageData >= 23X There is a 0.58% of reference with a coverageData >= 24X There is a 0.5% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.36% of reference with a coverageData >= 27X There is a 0.31% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1025238833 4.113284969508662 7.179692737492804 chr2 243199373 1075633603 4.422846941303586 22.204138089897892 chr3 198022430 873561326 4.411426150057849 4.503221145127456 chr4 191154276 816021187 4.268914115214456 4.87453828444744 chr5 180915260 778525429 4.30326015063627 4.328558662729054 chr6 171115067 741405939 4.332791682219311 4.787183385381326 chr7 159138663 653306667 4.105266782340631 4.81093190250263 chr8 146364022 649987563 4.440897114729466 4.5436381880057395 chr9 141213431 517049195 3.6614732135500625 5.441251759899239 chr10 135534747 693070563 5.113600595720299 7.313960266096484 chr11 135006516 589138606 4.363779049005308 4.6922422899512215 chr12 133851895 573976416 4.288145610489862 5.299061745473285 chr13 115169878 391784757 3.4017988366715124 3.9942194788997285 chr14 107349540 371943172 3.464785894750923 4.2623884616844965 chr15 102531392 350314938 3.4166603141406684 4.383132686389697 chr16 90354753 312926500 3.4633097829396977 4.314419278033412 chr17 81195210 276406700 3.404224214704291 4.742761020296002 chr18 78077248 323649559 4.145248036918514 5.483237657702884 chr19 59128983 194599725 3.2911055649308225 5.449710593072921 chr20 63025520 248793803 3.9475089297160895 5.055059479488266 chr21 48129895 152763487 3.1739833839238587 6.746987305625258 chr22 51304566 121908128 2.376165271527684 3.773892811354584 chrMT 16571 890764 53.754390199746545 15.070257650928719 chrX 155270560 802834553 5.170552312041639 5.285092782635527 chrY 59373566 11470281 0.19318834580358538 2.3404705173291056