BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779397.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 = 14,741,952 number of mapped reads = 14,035,053 (95.2%) number of supplementary alignments = 48,819 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,063,503 number of mapped paired reads (second in pair) = 6,971,550 number of mapped paired reads (both in pair) = 13,909,158 number of mapped paired reads (singletons) = 125,895 number of mapped bases = 1,114,458,067 bp number of sequenced bases = 1,114,197,255 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 418,716 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 238,026.4211 std insert size = 4,752,577.0545 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.1839 >>>>>>> ACTG content number of A's = 335,260,420 bp (30.09%) number of C's = 222,247,706 bp (19.95%) number of T's = 328,993,327 bp (29.53%) number of G's = 227,455,153 bp (20.41%) number of N's = 240,649 bp (0.02%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 3,716,811 number of insertions = 103,721 mapped reads with insertion percentage = 0.73% number of deletions = 123,849 mapped reads with deletion percentage = 0.87% homopolymer indels = 47.25% >>>>>>> Coverage mean coverageData = 0.36X std coverageData = 1.3954X There is a 19.69% of reference with a coverageData >= 1X There is a 8.54% of reference with a coverageData >= 2X There is a 3.83% of reference with a coverageData >= 3X There is a 1.82% of reference with a coverageData >= 4X There is a 0.9% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% 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 0.01% 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 88193374 0.3538341194343504 3.2801780169367776 chr2 243199373 107883266 0.44360009924861116 1.0796805835986003 chr3 198022430 48162968 0.24321976050894842 0.7429667661880017 chr4 191154276 64075782 0.3352045444173062 0.8479038777479123 chr5 180915260 115513802 0.6384967304582266 1.2201474057189539 chr6 171115067 52915581 0.3092397526864189 0.9995868671392646 chr7 159138663 100634381 0.6323691496641517 1.6442864195011548 chr8 146364022 66752062 0.45606878717776694 1.0520813478535287 chr9 141213431 51590444 0.36533666546208343 1.175564413009178 chr10 135534747 30448591 0.22465523914690305 1.3183172876459037 chr11 135006516 65859603 0.4878253654068075 1.187962205035536 chr12 133851895 45776146 0.3419910192530334 0.9015251187694137 chr13 115169878 44387163 0.38540600867876235 0.9638560816414901 chr14 107349540 30275604 0.28202826020493427 0.7995161714163223 chr15 102531392 25950674 0.2530997921104982 0.7741012839237068 chr16 90354753 10541351 0.11666625882979283 0.5554950567320861 chr17 81195210 31192024 0.3841608883085591 1.4897464111476721 chr18 78077248 28518288 0.36525734103743 1.2674764924727175 chr19 59128983 14868884 0.25146524167344464 1.8853607315092011 chr20 63025520 23034010 0.36547116152314174 0.9567226242324997 chr21 48129895 14759947 0.3066690047838251 0.8529649531980799 chr22 51304566 8368607 0.16311622244304727 0.64209475309493 chrMT 16571 598 0.03608714018465995 0.22786669955535999 chrX 155270560 39827245 0.2565022306868733 0.7787756443177616 chrY 59373566 4927672 0.0829943749715151 0.42945690685244364