BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779094.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 = 3,460,120 number of mapped reads = 3,350,657 (96.84%) number of supplementary alignments = 20,085 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,686,299 number of mapped paired reads (second in pair) = 1,664,358 number of mapped paired reads (both in pair) = 3,315,642 number of mapped paired reads (singletons) = 35,015 number of mapped bases = 334,687,930 bp number of sequenced bases = 334,611,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,675 duplication rate = 1.18% >>>>>>> Insert size mean insert size = 63,568.5295 std insert size = 2,433,895.0208 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.3133 >>>>>>> ACTG content number of A's = 102,652,550 bp (30.68%) number of C's = 64,328,706 bp (19.22%) number of T's = 102,319,933 bp (30.58%) number of G's = 65,173,062 bp (19.48%) number of N's = 137,327 bp (0.04%) GC percentage = 38.7% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 1,364,023 number of insertions = 28,486 mapped reads with insertion percentage = 0.84% number of deletions = 34,343 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.1081X std coverageData = 0.4626X There is a 7.64% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 23405039 0.09390162763125072 0.44207268877581707 chr2 243199373 37097467 0.1525393200746451 0.5356228052308935 chr3 198022430 15100147 0.07625473033534635 0.3536239497423919 chr4 191154276 21145530 0.11062023012239601 0.43524606687190415 chr5 180915260 22793170 0.1259881007273792 0.4575408388204842 chr6 171115067 25456898 0.1487706398174744 0.5044463090536915 chr7 159138663 30595407 0.19225627778461354 0.7900390864589409 chr8 146364022 25868776 0.17674272438345537 0.5585560581842498 chr9 141213431 10679832 0.07562901010457002 0.38354495712576814 chr10 135534747 8517552 0.0628440469217831 0.4579926892142149 chr11 135006516 10717759 0.07938697566271542 0.37346468675632366 chr12 133851895 16060534 0.11998734870358017 0.4628398250951362 chr13 115169878 7645670 0.06638602152552424 0.3335034367879834 chr14 107349540 13985221 0.13027741898102219 0.48520358852417644 chr15 102531392 5405213 0.05271763988145211 0.29939859878792124 chr16 90354753 6260458 0.06928753377257309 0.33484261177041286 chr17 81195210 5686298 0.07003243171610739 0.3456537220316953 chr18 78077248 9219955 0.11808760216548617 0.4405686143544119 chr19 59128983 3575683 0.060472594294408884 0.35033271158517953 chr20 63025520 8452800 0.13411710050151113 0.5048721574141175 chr21 48129895 3651821 0.0758742773072744 0.3562937130073011 chr22 51304566 1649287 0.03214698278511897 0.21974151159484703 chrMT 16571 0 0.0 0.0 chrX 155270560 21467511 0.13825873365820282 0.505616657294325 chrY 59373566 249902 0.004208977442924685 0.0923835481276172