BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779316.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 = 15,282,076 number of mapped reads = 14,120,986 (92.4%) number of supplementary alignments = 38,798 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,150,322 number of mapped paired reads (second in pair) = 6,970,664 number of mapped paired reads (both in pair) = 13,906,500 number of mapped paired reads (singletons) = 214,486 number of mapped bases = 1,123,549,069 bp number of sequenced bases = 1,123,327,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 561,030 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 37,418.8858 std insert size = 1,822,244.4032 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 52.9308 >>>>>>> ACTG content number of A's = 347,945,838 bp (30.97%) number of C's = 211,725,751 bp (18.85%) number of T's = 347,682,841 bp (30.95%) number of G's = 215,678,455 bp (19.2%) number of N's = 294,926 bp (0.03%) GC percentage = 38.05% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 4,314,741 number of insertions = 83,010 mapped reads with insertion percentage = 0.58% number of deletions = 106,539 mapped reads with deletion percentage = 0.74% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.3629X std coverageData = 1.5993X There is a 14.41% of reference with a coverageData >= 1X There is a 6.63% of reference with a coverageData >= 2X There is a 3.88% of reference with a coverageData >= 3X There is a 2.55% of reference with a coverageData >= 4X There is a 1.79% of reference with a coverageData >= 5X There is a 1.32% of reference with a coverageData >= 6X There is a 1% of reference with a coverageData >= 7X There is a 0.77% of reference with a coverageData >= 8X There is a 0.61% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 78331293 0.3142671929391101 1.5252861214922733 chr2 243199373 84571560 0.34774579784792453 1.387180938789401 chr3 198022430 80596401 0.407006423464251 1.5400173323102304 chr4 191154276 85421180 0.4468703593112403 1.873059981103314 chr5 180915260 79248436 0.43804174396344453 1.5425901929101686 chr6 171115067 57466304 0.3358342722677951 1.3936524248524806 chr7 159138663 103481245 0.6502583536220862 3.0096995006738516 chr8 146364022 82009898 0.5603145969847699 1.742202650499579 chr9 141213431 41086873 0.29095584399475427 1.2725933185219256 chr10 135534747 22792231 0.16816522334305903 1.243074892361698 chr11 135006516 53904927 0.39927648381060366 1.6734288473139585 chr12 133851895 59582965 0.44514098959898923 1.849359077496084 chr13 115169878 38706989 0.33608604673524095 1.3354720332335561 chr14 107349540 38206723 0.35590951763743 1.3273882400536674 chr15 102531392 25877778 0.2523888293645716 1.1553088657473203 chr16 90354753 16992805 0.1880676382348143 0.9127259691142511 chr17 81195210 15131826 0.18636353055802182 1.014221963196677 chr18 78077248 34378805 0.4403178375344377 1.8859485843384751 chr19 59128983 7930935 0.1341293997902856 0.9626341735445044 chr20 63025520 24669432 0.391419729658716 1.6860710057603947 chr21 48129895 12775224 0.2654322017531931 1.0643370631712132 chr22 51304566 6580153 0.12825667407458433 1.098325262233148 chrMT 16571 1677 0.10120089312654637 0.3447307699307644 chrX 155270560 72673398 0.46804363943815236 1.6709440812407699 chrY 59373566 1130011 0.019032223868783626 0.26586672460578337