BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264612.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 = 1,083,764,110 number of mapped reads = 1,070,976,371 (98.82%) number of supplementary alignments = 7,903,273 (0.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 536,829,196 number of mapped paired reads (second in pair) = 534,147,175 number of mapped paired reads (both in pair) = 1,064,944,708 number of mapped paired reads (singletons) = 6,031,663 number of mapped bases = 105,849,806,996 bp number of sequenced bases = 105,817,462,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 292,120,525 duplication rate = 22.39% >>>>>>> Insert size mean insert size = 123,965.3923 std insert size = 3,394,659.6226 median insert size = 311 >>>>>>> Mapping quality mean mapping quality = 53.6139 >>>>>>> ACTG content number of A's = 31,590,389,998 bp (29.85%) number of C's = 21,254,522,018 bp (20.09%) number of T's = 31,610,495,151 bp (29.87%) number of G's = 21,309,866,004 bp (20.14%) number of N's = 52,189,126 bp (0.05%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 612,077,885 number of insertions = 10,560,544 mapped reads with insertion percentage = 0.96% number of deletions = 13,772,177 mapped reads with deletion percentage = 1.25% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 34.1926X std coverageData = 434.5009X There is a 92.37% of reference with a coverageData >= 1X There is a 92.35% of reference with a coverageData >= 2X There is a 92.32% of reference with a coverageData >= 3X There is a 92.3% of reference with a coverageData >= 4X There is a 92.27% of reference with a coverageData >= 5X There is a 92.24% of reference with a coverageData >= 6X There is a 92.19% of reference with a coverageData >= 7X There is a 92.13% of reference with a coverageData >= 8X There is a 92.05% of reference with a coverageData >= 9X There is a 91.92% of reference with a coverageData >= 10X There is a 91.75% of reference with a coverageData >= 11X There is a 91.52% of reference with a coverageData >= 12X There is a 91.22% of reference with a coverageData >= 13X There is a 90.84% of reference with a coverageData >= 14X There is a 90.39% of reference with a coverageData >= 15X There is a 89.86% of reference with a coverageData >= 16X There is a 89.26% of reference with a coverageData >= 17X There is a 88.59% of reference with a coverageData >= 18X There is a 87.86% of reference with a coverageData >= 19X There is a 87.05% of reference with a coverageData >= 20X There is a 86.15% of reference with a coverageData >= 21X There is a 85.13% of reference with a coverageData >= 22X There is a 83.96% of reference with a coverageData >= 23X There is a 82.58% of reference with a coverageData >= 24X There is a 80.96% of reference with a coverageData >= 25X There is a 79.05% of reference with a coverageData >= 26X There is a 76.81% of reference with a coverageData >= 27X There is a 74.2% of reference with a coverageData >= 28X There is a 71.23% of reference with a coverageData >= 29X There is a 67.88% of reference with a coverageData >= 30X There is a 64.18% of reference with a coverageData >= 31X There is a 60.17% of reference with a coverageData >= 32X There is a 55.91% of reference with a coverageData >= 33X There is a 51.46% of reference with a coverageData >= 34X There is a 46.91% of reference with a coverageData >= 35X There is a 42.33% of reference with a coverageData >= 36X There is a 37.81% of reference with a coverageData >= 37X There is a 33.43% of reference with a coverageData >= 38X There is a 29.26% of reference with a coverageData >= 39X There is a 25.35% of reference with a coverageData >= 40X There is a 21.74% of reference with a coverageData >= 41X There is a 18.47% of reference with a coverageData >= 42X There is a 15.54% of reference with a coverageData >= 43X There is a 12.97% of reference with a coverageData >= 44X There is a 10.73% of reference with a coverageData >= 45X There is a 8.82% of reference with a coverageData >= 46X There is a 7.2% of reference with a coverageData >= 47X There is a 5.86% of reference with a coverageData >= 48X There is a 4.75% of reference with a coverageData >= 49X There is a 3.84% of reference with a coverageData >= 50X There is a 3.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8581313460 34.42845368076335 856.8520176143439 chr2 243199373 8993437544 36.979690502738265 192.3770621339969 chr3 198022430 7040435503 35.55372743885629 32.5323778740031 chr4 191154276 7220822223 37.77484016627491 256.03775349558134 chr5 180915260 6459077631 35.70222672758506 29.28776620577318 chr6 171115067 6173019453 36.07525369463812 193.85678002266462 chr7 159138663 5743917592 36.09379068366309 298.2129947700133 chr8 146364022 5381169614 36.7656582571911 591.3529860056875 chr9 141213431 4447258757 31.49317119134369 280.48790317453194 chr10 135534747 5521471007 40.738416747109135 711.9064912358764 chr11 135006516 4770328055 35.334057913175094 141.49833923528334 chr12 133851895 4656347372 34.78731004891638 21.097552263674476 chr13 115169878 3457183602 30.018123332560968 17.102524109029876 chr14 107349540 3156642464 29.405272384026983 24.874512159956673 chr15 102531392 2931752274 28.593704004330693 18.23504195068399 chr16 90354753 3139175803 34.74278550681224 220.74114895029913 chr17 81195210 2773988103 34.164430426376136 122.2545476414342 chr18 78077248 2947610741 37.7524927748478 434.97162227084806 chr19 59128983 1995892132 33.75488687163789 364.6826975106955 chr20 63025520 2112276585 33.51462367942383 48.90779978376772 chr21 48129895 1472779786 30.600103864760147 98.33141690784029 chr22 51304566 1208762624 23.5605272248088 102.8007725314249 chrMT 16571 1763361275 106412.48415907308 14405.030840622796 chrX 155270560 2836598989 18.26874965221997 56.94469360431174 chrY 59373566 1065184407 17.94038119590122 264.32042514751333