BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779297.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 = 18,928,918 number of mapped reads = 17,901,180 (94.57%) number of supplementary alignments = 42,099 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,022,981 number of mapped paired reads (second in pair) = 8,878,199 number of mapped paired reads (both in pair) = 17,727,212 number of mapped paired reads (singletons) = 173,968 number of mapped bases = 1,425,337,104 bp number of sequenced bases = 1,425,069,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 904,749 duplication rate = 4.68% >>>>>>> Insert size mean insert size = 34,248.2938 std insert size = 1,759,497.7868 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 52.8631 >>>>>>> ACTG content number of A's = 439,051,806 bp (30.81%) number of C's = 271,428,700 bp (19.05%) number of T's = 438,053,058 bp (30.74%) number of G's = 276,157,204 bp (19.38%) number of N's = 378,479 bp (0.03%) GC percentage = 38.43% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,897,642 number of insertions = 102,755 mapped reads with insertion percentage = 0.57% number of deletions = 131,106 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.4604X std coverageData = 2.0272X There is a 15.27% of reference with a coverageData >= 1X There is a 8.04% of reference with a coverageData >= 2X There is a 5.05% of reference with a coverageData >= 3X There is a 3.48% of reference with a coverageData >= 4X There is a 2.54% of reference with a coverageData >= 5X There is a 1.92% of reference with a coverageData >= 6X There is a 1.5% of reference with a coverageData >= 7X There is a 1.19% of reference with a coverageData >= 8X There is a 0.97% of reference with a coverageData >= 9X There is a 0.79% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.47% of reference with a coverageData >= 13X There is a 0.4% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.19% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.13% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 115623082 0.4638828241876276 2.3054498473113934 chr2 243199373 119145230 0.48990763639838825 1.9183755754572034 chr3 198022430 102412166 0.5171745746176329 1.9448051715257881 chr4 191154276 105051029 0.5495614913683646 2.338956507925838 chr5 180915260 105344153 0.5822845071222847 2.1647268568320626 chr6 171115067 70058971 0.40942607935279013 1.6121887807911834 chr7 159138663 137739953 0.8655341851150277 3.4242380343633148 chr8 146364022 105668795 0.7219588089756102 2.1942825668736976 chr9 141213431 54107236 0.38315927611729794 1.508600909219757 chr10 135534747 30852817 0.2276376920525037 1.6809588251499854 chr11 135006516 67144296 0.49734115055602207 1.952145077382502 chr12 133851895 58373147 0.43610250717780275 1.975362700822161 chr13 115169878 51846746 0.4501762691803841 1.8970285009785506 chr14 107349540 50876602 0.4739340475981546 1.8912309921474775 chr15 102531392 26567263 0.2591134527852699 1.4045397917419438 chr16 90354753 17706041 0.1959613679647821 1.0000359561604086 chr17 81195210 19074813 0.2349253484288051 1.0466164295522347 chr18 78077248 41403060 0.5302832907225419 2.1221372594530834 chr19 59128983 9259824 0.15660380967485946 0.9961631459092419 chr20 63025520 28714180 0.4555960823488644 1.6323019264910623 chr21 48129895 20492087 0.4257662934855769 2.090185403367491 chr22 51304566 6387609 0.12450371376302062 0.6545310260843169 chrMT 16571 5429 0.32762054191056666 0.6467937605810236 chrX 155270560 80286000 0.5170716200160546 2.5598040041811014 chrY 59373566 1196575 0.020153328839975688 0.32534699968817615