BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779420.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 = 13,722,832 number of mapped reads = 13,326,024 (97.11%) number of supplementary alignments = 48,658 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,710,951 number of mapped paired reads (second in pair) = 6,615,073 number of mapped paired reads (both in pair) = 13,203,762 number of mapped paired reads (singletons) = 122,262 number of mapped bases = 1,059,853,927 bp number of sequenced bases = 1,059,630,935 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 490,062 duplication rate = 3.33% >>>>>>> Insert size mean insert size = 143,891.4476 std insert size = 3,618,439.4517 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.1988 >>>>>>> ACTG content number of A's = 322,571,350 bp (30.44%) number of C's = 207,558,923 bp (19.59%) number of T's = 316,026,229 bp (29.82%) number of G's = 213,239,149 bp (20.12%) number of N's = 235,284 bp (0.02%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.0034 number of mismatches = 3,458,914 number of insertions = 94,814 mapped reads with insertion percentage = 0.7% number of deletions = 107,789 mapped reads with deletion percentage = 0.8% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.3424X std coverageData = 1.4341X There is a 16.03% of reference with a coverageData >= 1X There is a 7.54% of reference with a coverageData >= 2X There is a 4.01% of reference with a coverageData >= 3X There is a 2.32% of reference with a coverageData >= 4X There is a 1.41% of reference with a coverageData >= 5X There is a 0.88% of reference with a coverageData >= 6X There is a 0.57% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 102790227 0.4123970748301566 2.8621365847237894 chr2 243199373 59499611 0.24465363650423555 0.9590755566171681 chr3 198022430 82084353 0.4145204813414319 1.1415662681542695 chr4 191154276 72441235 0.3789673792073581 1.0846457679218078 chr5 180915260 78710597 0.435068865943094 1.1433635848544883 chr6 171115067 56358569 0.3293606459564429 1.2381782658299156 chr7 159138663 135783385 0.8532394481660311 2.436401896468118 chr8 146364022 62394239 0.42629491966270233 1.2392785358343132 chr9 141213431 54715139 0.38746412867767516 1.430289240615841 chr10 135534747 23732042 0.17509931973385393 1.3697947532980776 chr11 135006516 33145362 0.24550935008203603 0.9678967292789445 chr12 133851895 34326025 0.25644780748154516 0.8368026560936311 chr13 115169878 29283179 0.2542607451576879 0.9688959339184902 chr14 107349540 40653209 0.37869942432915876 1.2021643739913503 chr15 102531392 27304191 0.26630079302931925 0.9819753979981201 chr16 90354753 22923942 0.25371041631866337 0.9018182440362749 chr17 81195210 20732752 0.25534452093910465 1.1763214881632285 chr18 78077248 33657075 0.43107404349087713 1.467197803637468 chr19 59128983 18892085 0.3195063409089921 1.7360661815261778 chr20 63025520 18108694 0.28732319860272476 0.9495757922784852 chr21 48129895 12270679 0.25494921607454163 0.942671096953544 chr22 51304566 10739146 0.20932144713981207 0.8116862101793388 chrMT 16571 80 0.00482771106149297 0.06931381007706695 chrX 155270560 25469562 0.16403342655555567 0.7146535146280149 chrY 59373566 3838549 0.0646508077348765 0.4068945841890154