BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779315.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 = 15,966,424 number of mapped reads = 15,108,303 (94.63%) number of supplementary alignments = 36,918 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,665,626 number of mapped paired reads (second in pair) = 7,442,677 number of mapped paired reads (both in pair) = 14,859,602 number of mapped paired reads (singletons) = 248,701 number of mapped bases = 1,202,552,934 bp number of sequenced bases = 1,202,319,726 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 465,002 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 41,797.2775 std insert size = 1,935,108.5029 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 53.1189 >>>>>>> ACTG content number of A's = 369,714,439 bp (30.75%) number of C's = 229,455,310 bp (19.08%) number of T's = 369,682,087 bp (30.75%) number of G's = 233,155,187 bp (19.39%) number of N's = 312,703 bp (0.03%) GC percentage = 38.48% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 4,462,568 number of insertions = 87,915 mapped reads with insertion percentage = 0.58% number of deletions = 112,185 mapped reads with deletion percentage = 0.73% homopolymer indels = 47.14% >>>>>>> Coverage mean coverageData = 0.3885X std coverageData = 1.4292X There is a 17.43% of reference with a coverageData >= 1X There is a 7.68% of reference with a coverageData >= 2X There is a 4.2% of reference with a coverageData >= 3X There is a 2.58% of reference with a coverageData >= 4X There is a 1.7% of reference with a coverageData >= 5X There is a 1.17% of reference with a coverageData >= 6X There is a 0.84% of reference with a coverageData >= 7X There is a 0.62% of reference with a coverageData >= 8X There is a 0.47% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 93085999 0.37346345869284714 1.4339677372922908 chr2 243199373 93918261 0.38617805564819446 1.2933541500063657 chr3 198022430 89249192 0.4507024381025927 1.3944336254682204 chr4 191154276 95041011 0.49719531777567977 1.4818359942834656 chr5 180915260 84861535 0.46906786635908987 1.4817057662828246 chr6 171115067 75741089 0.44263249477616134 1.3193229193374179 chr7 159138663 118096443 0.7420977452851919 2.919060070968232 chr8 146364022 85826804 0.5863927680260111 1.612327864477475 chr9 141213431 36941651 0.2616015398705241 0.9490897145018995 chr10 135534747 24138467 0.17809799726117465 1.0079054622242138 chr11 135006516 51417047 0.38084863252081846 1.4003043879354864 chr12 133851895 54791629 0.40934518708158746 1.4770115333055842 chr13 115169878 44390518 0.38543513955966857 1.277667859022695 chr14 107349540 36390522 0.33899094490763537 1.2310270513662396 chr15 102531392 27548899 0.26868745720335097 1.0309035003182603 chr16 90354753 20817405 0.23039634672013326 0.8969491906463722 chr17 81195210 14243133 0.17541838982866106 0.7030511600129837 chr18 78077248 32513638 0.4164290985256038 1.2869973566892765 chr19 59128983 9626069 0.1627978110159615 0.7749870726049205 chr20 63025520 19419589 0.3081226303249858 1.0736895604850862 chr21 48129895 13438973 0.2792229860464063 1.0193875945003257 chr22 51304566 4623925 0.09012696842616308 0.5904243501717175 chrMT 16571 1082 0.06529479210669241 0.3817822826685883 chrX 155270560 75638791 0.48714187029402095 1.6064128947301928 chrY 59373566 791262 0.013326839758959399 0.19487326809244102