BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779388.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 6,306,228 number of mapped reads = 3,369,770 (53.44%) number of supplementary alignments = 22,495 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,709,054 number of mapped paired reads (second in pair) = 1,660,716 number of mapped paired reads (both in pair) = 3,253,728 number of mapped paired reads (singletons) = 116,042 number of mapped bases = 265,749,126 bp number of sequenced bases = 265,686,977 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,819 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 54,893.2714 std insert size = 2,126,314.3728 median insert size = 351 >>>>>>> Mapping quality mean mapping quality = 51.7111 >>>>>>> ACTG content number of A's = 83,713,128 bp (31.51%) number of C's = 46,983,486 bp (17.68%) number of T's = 80,227,638 bp (30.2%) number of G's = 54,707,874 bp (20.59%) number of N's = 54,851 bp (0.02%) GC percentage = 38.27% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,904,916 number of insertions = 27,458 mapped reads with insertion percentage = 0.81% number of deletions = 30,620 mapped reads with deletion percentage = 0.9% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.0858X std coverageData = 0.9607X There is a 4.88% of reference with a coverageData >= 1X There is a 1.61% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17524282 0.07030787698619215 1.408593461133919 chr2 243199373 23101800 0.09499119884655295 0.829691860520512 chr3 198022430 18580623 0.09383090087319906 0.69346722075176 chr4 191154276 23752375 0.12425761796717537 0.8376996158490043 chr5 180915260 26051653 0.14399920161516502 0.7975426527977486 chr6 171115067 10706574 0.06256944048065621 0.48376577702511886 chr7 159138663 29553705 0.1857104015006083 0.9519482025874337 chr8 146364022 13260206 0.09059744204077694 0.6300479162034371 chr9 141213431 9950514 0.07046435972510291 0.5934328099772667 chr10 135534747 6625032 0.048880690351677865 1.1914041972485445 chr11 135006516 11778388 0.08724310758452578 0.5552665784343738 chr12 133851895 10871920 0.08122350453088467 0.4975002910150764 chr13 115169878 10295108 0.08939063042161076 0.6307271673569284 chr14 107349540 7765412 0.07233763647240593 0.7223095829766347 chr15 102531392 5181380 0.050534571889943716 0.5006653436016497 chr16 90354753 6443737 0.0713159716124729 0.9774869810045417 chr17 81195210 3556292 0.043799283233579914 0.5029769349533932 chr18 78077248 7716220 0.0988280222171765 0.8446169474994042 chr19 59128983 2064708 0.034918713213788914 0.9789180576869797 chr20 63025520 4244804 0.0673505589481848 3.5395880103380506 chr21 48129895 3773108 0.07839427033863257 0.5858466811318384 chr22 51304566 1489539 0.029033263822950964 1.1979664243937096 chrMT 16571 27491 1.6589825598937904 1.670602750037477 chrX 155270560 10009635 0.06446576221532273 0.6019440835883001 chrY 59373566 1424620 0.023994179497320408 0.2868889272635542