BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779330.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 = 152,400,940 number of mapped reads = 150,024,676 (98.44%) number of supplementary alignments = 501,515 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 75,494,797 number of mapped paired reads (second in pair) = 74,529,879 number of mapped paired reads (both in pair) = 148,935,820 number of mapped paired reads (singletons) = 1,088,856 number of mapped bases = 14,978,197,137 bp number of sequenced bases = 14,974,957,599 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,331,049 duplication rate = 7.33% >>>>>>> Insert size mean insert size = 43,255.7493 std insert size = 1,975,417.4486 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.8027 >>>>>>> ACTG content number of A's = 4,540,049,957 bp (30.32%) number of C's = 2,940,601,726 bp (19.64%) number of T's = 4,500,326,742 bp (30.05%) number of G's = 2,990,194,142 bp (19.97%) number of N's = 3,785,032 bp (0.03%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 43,099,070 number of insertions = 1,143,562 mapped reads with insertion percentage = 0.75% number of deletions = 1,466,086 mapped reads with deletion percentage = 0.96% homopolymer indels = 46.96% >>>>>>> Coverage mean coverageData = 4.8384X std coverageData = 6.8715X There is a 79.37% of reference with a coverageData >= 1X There is a 67.95% of reference with a coverageData >= 2X There is a 56.91% of reference with a coverageData >= 3X There is a 47.13% of reference with a coverageData >= 4X There is a 38.78% of reference with a coverageData >= 5X There is a 31.82% of reference with a coverageData >= 6X There is a 26.12% of reference with a coverageData >= 7X There is a 21.46% of reference with a coverageData >= 8X There is a 17.68% of reference with a coverageData >= 9X There is a 14.62% of reference with a coverageData >= 10X There is a 12.12% of reference with a coverageData >= 11X There is a 10.09% of reference with a coverageData >= 12X There is a 8.43% of reference with a coverageData >= 13X There is a 7.07% of reference with a coverageData >= 14X There is a 5.95% of reference with a coverageData >= 15X There is a 5.03% of reference with a coverageData >= 16X There is a 4.26% of reference with a coverageData >= 17X There is a 3.63% of reference with a coverageData >= 18X There is a 3.1% of reference with a coverageData >= 19X There is a 2.65% of reference with a coverageData >= 20X There is a 2.28% of reference with a coverageData >= 21X There is a 1.96% of reference with a coverageData >= 22X There is a 1.7% of reference with a coverageData >= 23X There is a 1.47% of reference with a coverageData >= 24X There is a 1.28% of reference with a coverageData >= 25X There is a 1.11% of reference with a coverageData >= 26X There is a 0.97% of reference with a coverageData >= 27X There is a 0.85% of reference with a coverageData >= 28X There is a 0.75% of reference with a coverageData >= 29X There is a 0.66% of reference with a coverageData >= 30X There is a 0.58% of reference with a coverageData >= 31X There is a 0.52% of reference with a coverageData >= 32X There is a 0.46% of reference with a coverageData >= 33X There is a 0.41% of reference with a coverageData >= 34X There is a 0.36% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1151057640 4.618073308631796 8.294317070598417 chr2 243199373 1249295298 5.1369182518410526 6.03482967520487 chr3 198022430 1051875754 5.3119020607918 5.551485499415805 chr4 191154276 1059315864 5.541680187159402 5.752426654489208 chr5 180915260 942040984 5.207084156416656 5.303940155830283 chr6 171115067 914756992 5.345858830771459 5.811212319479838 chr7 159138663 768834959 4.831226708244998 6.719927283291337 chr8 146364022 787658519 5.381503652584787 5.625895798439399 chr9 141213431 594295735 4.208492993842774 6.04943455924188 chr10 135534747 771602491 5.6930234355327345 15.383101262440858 chr11 135006516 677412643 5.017629245391386 5.77907062945326 chr12 133851895 1013506868 7.571852964801133 7.986540963651605 chr13 115169878 475939665 4.132501251759597 4.9339654562648505 chr14 107349540 391490129 3.646872906954236 4.907418426144557 chr15 102531392 397293556 3.874847968512902 5.373495757872207 chr16 90354753 286142608 3.1668794224914762 4.419691440370989 chr17 81195210 276399889 3.4041403304456015 4.8356643486838875 chr18 78077248 396182647 5.074239386613627 5.765354912771738 chr19 59128983 149748976 2.5325816275243564 5.574307525120005 chr20 63025520 253003157 4.014297018096796 5.749798471201652 chr21 48129895 170817369 3.5490908301379007 5.297236140681719 chr22 51304566 95523216 1.8618852754743116 3.5557998023426496 chrMT 16571 122354 7.383621990223885 3.590054177940226 chrX 155270560 1094479543 7.048854225810739 7.607086402946642 chrY 59373566 9400281 0.15832434588820216 1.4694168209814191