BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781857.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 = 147,673,722 number of mapped reads = 144,839,944 (98.08%) number of supplementary alignments = 452,134 (0.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 72,798,555 number of mapped paired reads (second in pair) = 72,041,389 number of mapped paired reads (both in pair) = 143,608,712 number of mapped paired reads (singletons) = 1,231,232 number of mapped bases = 14,393,275,040 bp number of sequenced bases = 14,390,286,594 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,836,715 duplication rate = 5.88% >>>>>>> Insert size mean insert size = 33,606.4198 std insert size = 1,783,281.0814 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.9284 >>>>>>> ACTG content number of A's = 4,287,562,664 bp (29.79%) number of C's = 2,896,423,927 bp (20.13%) number of T's = 4,272,695,712 bp (29.69%) number of G's = 2,932,124,542 bp (20.38%) number of N's = 1,479,749 bp (0.01%) GC percentage = 40.5% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 53,416,170 number of insertions = 1,628,865 mapped reads with insertion percentage = 1.11% number of deletions = 1,335,770 mapped reads with deletion percentage = 0.91% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 4.6495X std coverageData = 5.8613X There is a 81.86% of reference with a coverageData >= 1X There is a 70.21% of reference with a coverageData >= 2X There is a 58.35% of reference with a coverageData >= 3X There is a 47.57% of reference with a coverageData >= 4X There is a 38.36% of reference with a coverageData >= 5X There is a 30.76% of reference with a coverageData >= 6X There is a 24.63% of reference with a coverageData >= 7X There is a 19.75% of reference with a coverageData >= 8X There is a 15.88% of reference with a coverageData >= 9X There is a 12.83% of reference with a coverageData >= 10X There is a 10.4% of reference with a coverageData >= 11X There is a 8.48% of reference with a coverageData >= 12X There is a 6.95% of reference with a coverageData >= 13X There is a 5.72% of reference with a coverageData >= 14X There is a 4.73% of reference with a coverageData >= 15X There is a 3.94% of reference with a coverageData >= 16X There is a 3.29% of reference with a coverageData >= 17X There is a 2.76% of reference with a coverageData >= 18X There is a 2.32% of reference with a coverageData >= 19X There is a 1.97% of reference with a coverageData >= 20X There is a 1.67% of reference with a coverageData >= 21X There is a 1.43% of reference with a coverageData >= 22X There is a 1.22% of reference with a coverageData >= 23X There is a 1.05% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.78% of reference with a coverageData >= 26X There is a 0.68% of reference with a coverageData >= 27X There is a 0.59% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.45% of reference with a coverageData >= 30X There is a 0.4% of reference with a coverageData >= 31X There is a 0.35% of reference with a coverageData >= 32X There is a 0.31% of reference with a coverageData >= 33X There is a 0.28% of reference with a coverageData >= 34X There is a 0.25% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.14% of reference with a coverageData >= 40X There is a 0.13% of reference with a coverageData >= 41X There is a 0.12% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.06% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1138917157 4.569365373817865 6.722110424235067 chr2 243199373 1200172564 4.93493280511048 7.958391920695365 chr3 198022430 1026389755 5.183199473918182 5.1193461028634895 chr4 191154276 978327930 5.11800180708487 5.217413877487781 chr5 180915260 903560880 4.994387317023451 4.874386573727358 chr6 171115067 866802811 5.0656136025707195 5.256757384688364 chr7 159138663 756389812 4.7530235440020006 5.414045954069781 chr8 146364022 732472937 5.00446029694374 4.968258144253304 chr9 141213431 305791234 2.1654543185768214 4.139529030160567 chr10 135534747 795002550 5.865673324346855 7.712060967307853 chr11 135006516 644524982 4.774028699474031 5.113020341299837 chr12 133851895 977946523 7.306183621830681 7.199952565656388 chr13 115169878 465732838 4.043877149891571 4.631096784393564 chr14 107349540 431116398 4.016006011763069 4.775080442142516 chr15 102531392 402162737 3.922337629045356 4.885317943999795 chr16 90354753 322865572 3.573310327128004 4.634748982297428 chr17 81195210 298586608 3.6773919052614064 4.58824412329669 chr18 78077248 367356297 4.7050364403212575 5.314478774212593 chr19 59128983 188581309 3.1893210306018625 4.812396585555221 chr20 63025520 272601422 4.325254627014581 5.8239435780434405 chr21 48129895 169942901 3.5309219145398094 6.124914798642897 chr22 51304566 124858725 2.4336766633987312 3.9940094739169245 chrMT 16571 223508 13.487900549152133 5.536193737642363 chrX 155270560 1010173847 6.505894272552376 6.576596743677588 chrY 59373566 12773743 0.2151419202275976 2.21805205675054