BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781810.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 = 160,906,540 number of mapped reads = 157,650,362 (97.98%) number of supplementary alignments = 562,027 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 79,475,430 number of mapped paired reads (second in pair) = 78,174,932 number of mapped paired reads (both in pair) = 155,825,320 number of mapped paired reads (singletons) = 1,825,042 number of mapped bases = 15,656,444,546 bp number of sequenced bases = 15,653,192,012 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,471,599 duplication rate = 5.77% >>>>>>> Insert size mean insert size = 40,524.7056 std insert size = 1,970,576.4277 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 54.0309 >>>>>>> ACTG content number of A's = 4,605,306,847 bp (29.42%) number of C's = 3,204,492,468 bp (20.47%) number of T's = 4,590,629,303 bp (29.33%) number of G's = 3,251,477,460 bp (20.77%) number of N's = 1,285,934 bp (0.01%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 67,673,597 number of insertions = 1,454,354 mapped reads with insertion percentage = 0.91% number of deletions = 1,444,969 mapped reads with deletion percentage = 0.9% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 5.0575X std coverageData = 6.0253X There is a 84.42% of reference with a coverageData >= 1X There is a 74.49% of reference with a coverageData >= 2X There is a 63.45% of reference with a coverageData >= 3X There is a 52.76% of reference with a coverageData >= 4X There is a 43.16% of reference with a coverageData >= 5X There is a 34.96% of reference with a coverageData >= 6X There is a 28.16% of reference with a coverageData >= 7X There is a 22.61% of reference with a coverageData >= 8X There is a 18.16% of reference with a coverageData >= 9X There is a 14.6% of reference with a coverageData >= 10X There is a 11.76% of reference with a coverageData >= 11X There is a 9.51% of reference with a coverageData >= 12X There is a 7.71% of reference with a coverageData >= 13X There is a 6.28% of reference with a coverageData >= 14X There is a 5.13% of reference with a coverageData >= 15X There is a 4.21% of reference with a coverageData >= 16X There is a 3.47% of reference with a coverageData >= 17X There is a 2.87% of reference with a coverageData >= 18X There is a 2.39% of reference with a coverageData >= 19X There is a 1.99% of reference with a coverageData >= 20X There is a 1.67% of reference with a coverageData >= 21X There is a 1.41% of reference with a coverageData >= 22X There is a 1.19% of reference with a coverageData >= 23X There is a 1.01% of reference with a coverageData >= 24X There is a 0.86% of reference with a coverageData >= 25X There is a 0.74% of reference with a coverageData >= 26X There is a 0.63% of reference with a coverageData >= 27X There is a 0.55% of reference with a coverageData >= 28X There is a 0.47% of reference with a coverageData >= 29X There is a 0.41% of reference with a coverageData >= 30X There is a 0.36% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.28% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.14% of reference with a coverageData >= 39X There is a 0.13% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.09% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1289979498 5.175431430519886 8.590978118814812 chr2 243199373 1318703694 5.422315352762032 6.119505018973923 chr3 198022430 1086493094 5.486717307731251 5.091633375888653 chr4 191154276 989217113 5.1749672238564 5.531465742296444 chr5 180915260 965865928 5.338775336033014 4.891334380130126 chr6 171115067 913812162 5.340337224658305 5.458762375846072 chr7 159138663 808129032 5.0781439077441535 5.511877217767221 chr8 146364022 790581105 5.401471578855629 5.187042100809577 chr9 141213431 653345789 4.626654733712971 6.122874982116291 chr10 135534747 886943577 6.544030934001006 8.711115681019308 chr11 135006516 732105548 5.422742321563205 5.331102933972485 chr12 133851895 714687211 5.339388067684809 5.193287856438143 chr13 115169878 482950404 4.193374277951393 4.566582606024829 chr14 107349540 471826545 4.395235834266267 4.906315489261738 chr15 102531392 448325720 4.372570305102266 5.01569597151887 chr16 90354753 400996425 4.438022480123431 5.184307190528789 chr17 81195210 369105052 4.5458968823407195 5.481897601889069 chr18 78077248 394144995 5.048141489310689 6.0071180990782125 chr19 59128983 244413702 4.133568507342668 6.283594975999819 chr20 63025520 319139919 5.063661815086968 5.858758228156996 chr21 48129895 186740355 3.879924421193938 7.646086578479101 chr22 51304566 159061216 3.100332551297676 4.592389194848474 chrMT 16571 274947 16.592058415303843 5.96837479556557 chrX 155270560 1015359374 6.539290989869555 6.140939108786038 chrY 59373566 14242141 0.23987343121684826 2.6867673909466494