BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779168.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 = 5,909,572 number of mapped reads = 5,740,060 (97.13%) number of supplementary alignments = 34,896 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,896,915 number of mapped paired reads (second in pair) = 2,843,145 number of mapped paired reads (both in pair) = 5,664,950 number of mapped paired reads (singletons) = 75,110 number of mapped bases = 573,629,173 bp number of sequenced bases = 573,495,782 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,319 duplication rate = 1.3% >>>>>>> Insert size mean insert size = 70,833.7655 std insert size = 2,525,903.759 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 53.6128 >>>>>>> ACTG content number of A's = 175,576,227 bp (30.62%) number of C's = 110,665,008 bp (19.3%) number of T's = 174,723,830 bp (30.47%) number of G's = 112,296,720 bp (19.58%) number of N's = 233,997 bp (0.04%) GC percentage = 38.88% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 2,430,093 number of insertions = 48,215 mapped reads with insertion percentage = 0.83% number of deletions = 59,556 mapped reads with deletion percentage = 1.02% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.1853X std coverageData = 0.6745X There is a 11.71% of reference with a coverageData >= 1X There is a 3.91% of reference with a coverageData >= 2X There is a 1.46% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 40863783 0.16394656445008415 0.6521576089154844 chr2 243199373 47278923 0.19440396748062339 0.6800157672030445 chr3 198022430 43019501 0.21724559687506106 0.6711912595453201 chr4 191154276 49064686 0.25667584856956066 0.7366829644938845 chr5 180915260 36592811 0.20226492226250015 0.6603915332247309 chr6 171115067 35434060 0.20707738144414833 0.6735371838546793 chr7 159138663 40091467 0.25192788631132335 0.9532005078945113 chr8 146364022 41847942 0.2859168628202906 0.7971032103668353 chr9 141213431 23084892 0.16347518671931427 0.6361834798971264 chr10 135534747 15172799 0.11194766903574918 0.7917553565481552 chr11 135006516 25542390 0.18919375713687775 0.6370110655616019 chr12 133851895 25566044 0.19100248076428056 0.6397615563044456 chr13 115169878 16400533 0.14240297276341649 0.5532227844301169 chr14 107349540 17207636 0.1602953864543807 0.581992164351277 chr15 102531392 15049841 0.14678276288300074 0.5683456715171218 chr16 90354753 9589847 0.10613550125027733 0.4568848081734977 chr17 81195210 10760852 0.13253062588298004 0.5446991903425699 chr18 78077248 14597955 0.1869681036913596 0.6273383636741904 chr19 59128983 5641904 0.09541689563644279 0.4808122165358207 chr20 63025520 12498384 0.19830671765976704 0.6575164367514522 chr21 48129895 6467316 0.13437211944883737 0.5218708494118287 chr22 51304566 3357562 0.06544372678252458 0.36184448474828423 chrMT 16571 467 0.02818176332146521 0.17263084043213314 chrX 155270560 38104829 0.24540923276118795 0.8080521999495894 chrY 59373566 392749 0.006614879759790746 0.13187100190394604