BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781845.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 357,630,720 number of mapped reads = 349,344,035 (97.68%) number of supplementary alignments = 1,347,981 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 175,646,172 number of mapped paired reads (second in pair) = 173,697,863 number of mapped paired reads (both in pair) = 346,186,112 number of mapped paired reads (singletons) = 3,157,923 number of mapped bases = 34,680,249,639 bp number of sequenced bases = 34,673,051,353 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,671,173 duplication rate = 10.43% >>>>>>> Insert size mean insert size = 41,101.0603 std insert size = 1,991,243.273 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 53.9793 >>>>>>> ACTG content number of A's = 10,188,078,150 bp (29.38%) number of C's = 7,127,133,518 bp (20.56%) number of T's = 10,164,076,885 bp (29.31%) number of G's = 7,189,900,670 bp (20.74%) number of N's = 3,862,130 bp (0.01%) GC percentage = 41.29% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 144,027,168 number of insertions = 3,235,714 mapped reads with insertion percentage = 0.91% number of deletions = 3,235,479 mapped reads with deletion percentage = 0.91% homopolymer indels = 46.38% >>>>>>> Coverage mean coverageData = 11.2027X std coverageData = 12.7077X There is a 89.97% of reference with a coverageData >= 1X There is a 87.27% of reference with a coverageData >= 2X There is a 83.51% of reference with a coverageData >= 3X There is a 78.88% of reference with a coverageData >= 4X There is a 73.62% of reference with a coverageData >= 5X There is a 68.03% of reference with a coverageData >= 6X There is a 62.34% of reference with a coverageData >= 7X There is a 56.75% of reference with a coverageData >= 8X There is a 51.39% of reference with a coverageData >= 9X There is a 46.35% of reference with a coverageData >= 10X There is a 41.68% of reference with a coverageData >= 11X There is a 37.4% of reference with a coverageData >= 12X There is a 33.51% of reference with a coverageData >= 13X There is a 30% of reference with a coverageData >= 14X There is a 26.85% of reference with a coverageData >= 15X There is a 24.02% of reference with a coverageData >= 16X There is a 21.5% of reference with a coverageData >= 17X There is a 19.25% of reference with a coverageData >= 18X There is a 17.24% of reference with a coverageData >= 19X There is a 15.46% of reference with a coverageData >= 20X There is a 13.87% of reference with a coverageData >= 21X There is a 12.46% of reference with a coverageData >= 22X There is a 11.2% of reference with a coverageData >= 23X There is a 10.08% of reference with a coverageData >= 24X There is a 9.08% of reference with a coverageData >= 25X There is a 8.19% of reference with a coverageData >= 26X There is a 7.39% of reference with a coverageData >= 27X There is a 6.68% of reference with a coverageData >= 28X There is a 6.05% of reference with a coverageData >= 29X There is a 5.48% of reference with a coverageData >= 30X There is a 4.97% of reference with a coverageData >= 31X There is a 4.51% of reference with a coverageData >= 32X There is a 4.1% of reference with a coverageData >= 33X There is a 3.73% of reference with a coverageData >= 34X There is a 3.4% of reference with a coverageData >= 35X There is a 3.1% of reference with a coverageData >= 36X There is a 2.83% of reference with a coverageData >= 37X There is a 2.59% of reference with a coverageData >= 38X There is a 2.37% of reference with a coverageData >= 39X There is a 2.17% of reference with a coverageData >= 40X There is a 1.99% of reference with a coverageData >= 41X There is a 1.82% of reference with a coverageData >= 42X There is a 1.67% of reference with a coverageData >= 43X There is a 1.54% of reference with a coverageData >= 44X There is a 1.42% of reference with a coverageData >= 45X There is a 1.3% of reference with a coverageData >= 46X There is a 1.2% of reference with a coverageData >= 47X There is a 1.11% of reference with a coverageData >= 48X There is a 1.03% of reference with a coverageData >= 49X There is a 0.95% of reference with a coverageData >= 50X There is a 0.88% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2895497575 11.616811879477725 17.256560686756185 chr2 243199373 2888170191 11.875730415637214 17.2189484277851 chr3 198022430 2398964932 12.114612127525149 10.078652512292313 chr4 191154276 2147333203 11.23350859804988 10.712446148381867 chr5 180915260 2096478192 11.588177757918265 9.593143343558548 chr6 171115067 2006489077 11.72596377500761 10.70535510503519 chr7 159138663 1767412136 11.106114018313702 11.057119334465428 chr8 146364022 1737558121 11.871483833643216 10.018841057988556 chr9 141213431 1411307036 9.994141676226251 12.25810930169574 chr10 135534747 1949452678 14.383416217245014 19.070202048288827 chr11 135006516 1579583574 11.70005434404366 10.535398201947093 chr12 133851895 2358327989 17.618936130863144 14.515934413940187 chr13 115169878 1026778555 8.9153394345004 8.995047913602892 chr14 107349540 1023880964 9.537823487646058 9.84797578987869 chr15 102531392 1026416819 10.010756695861497 10.43206481764487 chr16 90354753 838571192 9.280875262865253 9.80896809040146 chr17 81195210 839351467 10.337450534335709 10.890292712568675 chr18 78077248 815911004 10.450048188173845 11.509401557470193 chr19 59128983 531274254 8.985005779652933 12.490176156285099 chr20 63025520 699683954 11.101597479877992 11.513957626787702 chr21 48129895 382568156 7.948659684381194 13.88015705963624 chr22 51304566 351163611 6.844685344380459 9.443120042567635 chrMT 16571 3309647 199.72524289421278 51.957544972716036 chrX 155270560 1878564887 12.098654677358025 10.340230776352685 chrY 59373566 26200425 0.4412809734217413 4.811160784598146