BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264625.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,284,690,418 number of mapped reads = 1,278,712,945 (99.53%) number of supplementary alignments = 7,918,335 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 640,811,740 number of mapped paired reads (second in pair) = 637,901,205 number of mapped paired reads (both in pair) = 1,274,819,146 number of mapped paired reads (singletons) = 3,893,799 number of mapped bases = 128,449,668,153 bp number of sequenced bases = 128,419,799,994 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 444,697,130 duplication rate = 34.28% >>>>>>> Insert size mean insert size = 74,539.4517 std insert size = 2,635,428.9441 median insert size = 315 >>>>>>> Mapping quality mean mapping quality = 54.4768 >>>>>>> ACTG content number of A's = 39,749,580,378 bp (30.95%) number of C's = 24,413,944,381 bp (19.01%) number of T's = 39,648,937,231 bp (30.87%) number of G's = 24,595,485,672 bp (19.15%) number of N's = 11,852,332 bp (0.01%) GC percentage = 38.16% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 445,015,279 number of insertions = 14,043,440 mapped reads with insertion percentage = 1.08% number of deletions = 13,386,085 mapped reads with deletion percentage = 1.03% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 41.493X std coverageData = 43.1571X There is a 90.21% of reference with a coverageData >= 1X There is a 88.57% of reference with a coverageData >= 2X There is a 86.98% of reference with a coverageData >= 3X There is a 85.41% of reference with a coverageData >= 4X There is a 83.86% of reference with a coverageData >= 5X There is a 82.33% of reference with a coverageData >= 6X There is a 80.81% of reference with a coverageData >= 7X There is a 79.31% of reference with a coverageData >= 8X There is a 77.84% of reference with a coverageData >= 9X There is a 76.37% of reference with a coverageData >= 10X There is a 74.93% of reference with a coverageData >= 11X There is a 73.5% of reference with a coverageData >= 12X There is a 72.09% of reference with a coverageData >= 13X There is a 70.7% of reference with a coverageData >= 14X There is a 69.32% of reference with a coverageData >= 15X There is a 67.96% of reference with a coverageData >= 16X There is a 66.61% of reference with a coverageData >= 17X There is a 65.29% of reference with a coverageData >= 18X There is a 63.97% of reference with a coverageData >= 19X There is a 62.68% of reference with a coverageData >= 20X There is a 61.39% of reference with a coverageData >= 21X There is a 60.13% of reference with a coverageData >= 22X There is a 58.88% of reference with a coverageData >= 23X There is a 57.64% of reference with a coverageData >= 24X There is a 56.43% of reference with a coverageData >= 25X There is a 55.23% of reference with a coverageData >= 26X There is a 54.04% of reference with a coverageData >= 27X There is a 52.88% of reference with a coverageData >= 28X There is a 51.73% of reference with a coverageData >= 29X There is a 50.6% of reference with a coverageData >= 30X There is a 49.48% of reference with a coverageData >= 31X There is a 48.39% of reference with a coverageData >= 32X There is a 47.31% of reference with a coverageData >= 33X There is a 46.25% of reference with a coverageData >= 34X There is a 45.22% of reference with a coverageData >= 35X There is a 44.19% of reference with a coverageData >= 36X There is a 43.19% of reference with a coverageData >= 37X There is a 42.21% of reference with a coverageData >= 38X There is a 41.24% of reference with a coverageData >= 39X There is a 40.29% of reference with a coverageData >= 40X There is a 39.36% of reference with a coverageData >= 41X There is a 38.45% of reference with a coverageData >= 42X There is a 37.55% of reference with a coverageData >= 43X There is a 36.68% of reference with a coverageData >= 44X There is a 35.81% of reference with a coverageData >= 45X There is a 34.97% of reference with a coverageData >= 46X There is a 34.14% of reference with a coverageData >= 47X There is a 33.33% of reference with a coverageData >= 48X There is a 32.54% of reference with a coverageData >= 49X There is a 31.76% of reference with a coverageData >= 50X There is a 30.99% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10126606670 40.62821039069748 44.507621353380344 chr2 243199373 11946212591 49.12106657034843 44.8069515734705 chr3 198022430 9498278663 47.96567067175168 42.77507051878604 chr4 191154276 10693500143 55.94172605900796 45.086955253863344 chr5 180915260 9391797593 51.91268880800879 44.47259106323736 chr6 171115067 8590554361 50.203377829960466 44.03152407625907 chr7 159138663 7104574846 44.643926950674455 43.05520323907364 chr8 146364022 7274291465 49.69999707305119 43.93614078996728 chr9 141213431 5211086897 36.90220441566922 43.81918259380327 chr10 135534747 5411868928 39.929752685486626 38.335516634351855 chr11 135006516 6322736515 46.83282483195107 46.25691773894378 chr12 133851895 6012113378 44.916161836931785 45.03890480984452 chr13 115169878 5160989953 44.81197725155183 44.86966886562347 chr14 107349540 4069653019 37.91029769666456 43.00919773005581 chr15 102531392 3549620997 34.619845958982005 41.41139646701262 chr16 90354753 2359082108 26.10910914669868 32.619052637569034 chr17 81195210 2015136548 24.818416603639548 32.33299698003119 chr18 78077248 3856461543 49.39289795408773 43.445375978908665 chr19 59128983 958720186 16.21404829506369 24.240203659282543 chr20 63025520 1956211013 31.03839544679679 41.67074543494382 chr21 48129895 1786524119 37.11880358351083 48.3277572974914 chr22 51304566 661633251 12.896186491471344 22.247249812678426 chrMT 16571 38557 2.3267756924748055 8.912962342730811 chrX 155270560 3896987739 25.0980465260124 28.843832974443483 chrY 59373566 594987070 10.021076887987492 22.34523967034187