BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779213.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 = 7,546,502 number of mapped reads = 7,285,073 (96.54%) number of supplementary alignments = 15,718 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,685,986 number of mapped paired reads (second in pair) = 3,599,087 number of mapped paired reads (both in pair) = 7,189,144 number of mapped paired reads (singletons) = 95,929 number of mapped bases = 579,562,014 bp number of sequenced bases = 579,446,051 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,600 duplication rate = 0.77% >>>>>>> Insert size mean insert size = 53,312.8441 std insert size = 2,188,649.0371 median insert size = 275 >>>>>>> Mapping quality mean mapping quality = 52.7852 >>>>>>> ACTG content number of A's = 178,858,995 bp (30.87%) number of C's = 109,957,451 bp (18.98%) number of T's = 178,515,957 bp (30.81%) number of G's = 112,008,775 bp (19.33%) number of N's = 104,873 bp (0.02%) GC percentage = 38.31% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 2,484,873 number of insertions = 44,076 mapped reads with insertion percentage = 0.6% number of deletions = 55,676 mapped reads with deletion percentage = 0.75% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.1872X std coverageData = 0.5916X There is a 13.2% of reference with a coverageData >= 1X There is a 3.53% of reference with a coverageData >= 2X There is a 1.15% of reference with a coverageData >= 3X There is a 0.43% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% 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 45218263 0.1814168519162887 0.6179924714410968 chr2 243199373 44603606 0.18340345803440866 0.5461090108640336 chr3 198022430 48160899 0.24320931219761316 0.6431250636135992 chr4 191154276 47917392 0.25067392162339075 0.6470498196745775 chr5 180915260 26068565 0.14409268184452764 0.47694729778995576 chr6 171115067 35190814 0.2056558467759008 0.5911802285307043 chr7 159138663 50442288 0.3169706660159637 0.9391339918106424 chr8 146364022 53633193 0.36643699911444083 0.7968321130254112 chr9 141213431 21297817 0.15082005195384 0.527636806523748 chr10 135534747 8151163 0.06014076227994877 0.3509039796232178 chr11 135006516 26479892 0.1961378812264143 0.585061112239983 chr12 133851895 23389828 0.17474409308885766 0.5410745856385286 chr13 115169878 15915946 0.13819538820732274 0.472129181765163 chr14 107349540 23388698 0.2178742265686467 0.6260434764362084 chr15 102531392 12804048 0.12487929550395649 0.46251271803765853 chr16 90354753 7967337 0.08817839389146467 0.36806738206696055 chr17 81195210 7203041 0.08871263464926071 0.38431371239552264 chr18 78077248 21569061 0.2762528336039713 0.6761767502512098 chr19 59128983 3994424 0.0675544174334945 0.3526441657773953 chr20 63025520 8356855 0.13259478065393193 0.47158654269845884 chr21 48129895 2965910 0.06162303075874152 0.30554281252336724 chr22 51304566 2140590 0.041723186977159106 0.23838328888742183 chrMT 16571 1381 0.0833383621990224 0.42122802639829066 chrX 155270560 42279795 0.2722975623968897 0.7106053599334909 chrY 59373566 421208 0.0070942008098351375 0.10606371761469965