BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779309.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 = 16,686,288 number of mapped reads = 16,062,455 (96.26%) number of supplementary alignments = 44,179 (0.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,078,751 number of mapped paired reads (second in pair) = 7,983,704 number of mapped paired reads (both in pair) = 15,938,712 number of mapped paired reads (singletons) = 123,743 number of mapped bases = 1,278,559,491 bp number of sequenced bases = 1,278,305,709 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 551,984 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 36,106.4177 std insert size = 1,794,675.4093 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.0426 >>>>>>> ACTG content number of A's = 394,182,349 bp (30.84%) number of C's = 243,258,684 bp (19.03%) number of T's = 392,869,201 bp (30.73%) number of G's = 247,657,855 bp (19.37%) number of N's = 337,620 bp (0.03%) GC percentage = 38.4% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,474,359 number of insertions = 94,409 mapped reads with insertion percentage = 0.58% number of deletions = 123,072 mapped reads with deletion percentage = 0.76% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.413X std coverageData = 1.6035X There is a 16.81% of reference with a coverageData >= 1X There is a 8.04% of reference with a coverageData >= 2X There is a 4.62% of reference with a coverageData >= 3X There is a 2.96% of reference with a coverageData >= 4X There is a 2.01% of reference with a coverageData >= 5X There is a 1.43% of reference with a coverageData >= 6X There is a 1.05% of reference with a coverageData >= 7X There is a 0.79% 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 0.38% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.25% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.02% 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 0.01% 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 0.01% 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% 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 107634308 0.43183165429304987 1.961497781526306 chr2 243199373 104767282 0.4307876320059427 1.4766339262607155 chr3 198022430 89019806 0.449544054176085 1.582919542220038 chr4 191154276 104537751 0.5468763408672062 1.7891610422746278 chr5 180915260 66028697 0.36497030156549537 1.2570313746713524 chr6 171115067 75377395 0.4405070594981563 1.5075394341223367 chr7 159138663 108839440 0.683928329849045 2.1612001450741722 chr8 146364022 105464762 0.7205647983628107 1.984658349001069 chr9 141213431 50312621 0.35628778823453416 1.4584583167967702 chr10 135534747 28597849 0.21100012825493378 1.8903165593790248 chr11 135006516 58316031 0.43194975122534085 1.521771624791343 chr12 133851895 58465598 0.4367932034133697 1.4371720176439573 chr13 115169878 31423809 0.27284746277147226 1.1061317203588332 chr14 107349540 37908161 0.35312830404303547 1.2738694301582358 chr15 102531392 30122722 0.293790237432844 1.215397029459786 chr16 90354753 25890213 0.28653958026978393 1.1919919200288995 chr17 81195210 17554799 0.21620485986796512 0.9483438053282341 chr18 78077248 34095043 0.4366834625113836 1.6562395612517047 chr19 59128983 11150647 0.1885817484802673 1.1121237961519153 chr20 63025520 23868020 0.37870405511925964 1.2003971904739963 chr21 48129895 15210890 0.31603829594891075 1.3396787805682244 chr22 51304566 4537063 0.0884339027446407 0.5137024740345281 chrMT 16571 434 0.02619033250859936 0.16672600800684195 chrX 155270560 88337665 0.5689273291730255 2.2344461526160417 chrY 59373566 1098485 0.018501246834323543 0.32227933720656415