BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779229.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 = 13,487,208 number of mapped reads = 13,215,151 (97.98%) number of supplementary alignments = 34,410 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,637,071 number of mapped paired reads (second in pair) = 6,578,080 number of mapped paired reads (both in pair) = 13,139,662 number of mapped paired reads (singletons) = 75,489 number of mapped bases = 1,051,969,571 bp number of sequenced bases = 1,051,775,830 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 160,716 duplication rate = 1.15% >>>>>>> Insert size mean insert size = 55,321.5617 std insert size = 2,195,818.2474 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.0548 >>>>>>> ACTG content number of A's = 321,828,783 bp (30.6%) number of C's = 203,410,421 bp (19.34%) number of T's = 318,988,801 bp (30.33%) number of G's = 207,348,585 bp (19.71%) number of N's = 199,240 bp (0.02%) GC percentage = 39.05% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 3,868,194 number of insertions = 74,811 mapped reads with insertion percentage = 0.56% number of deletions = 93,645 mapped reads with deletion percentage = 0.7% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.3398X std coverageData = 0.8801X There is a 21.28% of reference with a coverageData >= 1X There is a 7.45% of reference with a coverageData >= 2X There is a 2.82% of reference with a coverageData >= 3X There is a 1.18% of reference with a coverageData >= 4X There is a 0.54% of reference with a coverageData >= 5X There is a 0.26% of reference with a coverageData >= 6X There is a 0.14% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% 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 75046846 0.3010899058101043 0.9625767115617846 chr2 243199373 61986780 0.2548805090874967 0.6773167517156325 chr3 198022430 74522121 0.37633171656362363 0.8314205891126856 chr4 191154276 72833451 0.3810192087986564 0.8358743495838619 chr5 180915260 83896025 0.46373105839717443 0.9254477242908334 chr6 171115067 51484776 0.3008780985954907 0.7461832511506671 chr7 159138663 88126909 0.5537743458357445 1.4116131630540463 chr8 146364022 74403978 0.5083488208598148 1.0206405554401499 chr9 141213431 41817188 0.2961275546091646 0.773392458117945 chr10 135534747 25283798 0.1865484575700724 0.9827622182392547 chr11 135006516 53055855 0.3929873651431758 0.8641482400431685 chr12 133851895 47375736 0.35394146642451346 0.8122932453328353 chr13 115169878 43918708 0.3813384954701437 0.853160009627275 chr14 107349540 38140659 0.3552941074549551 0.8368529642720921 chr15 102531392 27395439 0.26719074485987665 0.7170105165078631 chr16 90354753 22494100 0.24895314582952818 0.676754359467361 chr17 81195210 18138872 0.2233983014515265 0.6501632846171763 chr18 78077248 19436990 0.24894563394447508 0.6644191740632454 chr19 59128983 10309822 0.17436156478456596 0.6788356109673986 chr20 63025520 21570898 0.3422565652770497 0.8320469916012204 chr21 48129895 9131488 0.1897259073596566 0.6050120948477632 chr22 51304566 5630307 0.10974280534796844 0.43654847643004463 chrMT 16571 794 0.047915032285317724 0.21916440745969945 chrX 155270560 85269820 0.5491692694352361 1.1240929912316588 chrY 59373566 698211 0.01175962717145876 0.1532263287052034