BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781856.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 = 167,170,460 number of mapped reads = 163,943,846 (98.07%) number of supplementary alignments = 628,920 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 82,277,120 number of mapped paired reads (second in pair) = 81,666,726 number of mapped paired reads (both in pair) = 162,837,132 number of mapped paired reads (singletons) = 1,106,714 number of mapped bases = 16,280,566,357 bp number of sequenced bases = 16,277,216,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,595,882 duplication rate = 6.21% >>>>>>> Insert size mean insert size = 37,934.6188 std insert size = 1,902,032.396 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 53.9335 >>>>>>> ACTG content number of A's = 4,786,222,727 bp (29.4%) number of C's = 3,331,224,897 bp (20.47%) number of T's = 4,774,151,357 bp (29.33%) number of G's = 3,363,417,120 bp (20.66%) number of N's = 22,200,884 bp (0.14%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 81,320,110 number of insertions = 1,496,489 mapped reads with insertion percentage = 0.9% number of deletions = 1,494,221 mapped reads with deletion percentage = 0.9% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 5.2591X std coverageData = 6.5378X There is a 83.64% of reference with a coverageData >= 1X There is a 73.91% of reference with a coverageData >= 2X There is a 63.33% of reference with a coverageData >= 3X There is a 53.2% of reference with a coverageData >= 4X There is a 44.07% of reference with a coverageData >= 5X There is a 36.2% of reference with a coverageData >= 6X There is a 29.59% of reference with a coverageData >= 7X There is a 24.13% of reference with a coverageData >= 8X There is a 19.67% of reference with a coverageData >= 9X There is a 16.05% of reference with a coverageData >= 10X There is a 13.13% of reference with a coverageData >= 11X There is a 10.77% of reference with a coverageData >= 12X There is a 8.86% of reference with a coverageData >= 13X There is a 7.31% of reference with a coverageData >= 14X There is a 6.06% of reference with a coverageData >= 15X There is a 5.03% of reference with a coverageData >= 16X There is a 4.2% of reference with a coverageData >= 17X There is a 3.52% of reference with a coverageData >= 18X There is a 2.96% of reference with a coverageData >= 19X There is a 2.5% of reference with a coverageData >= 20X There is a 2.12% of reference with a coverageData >= 21X There is a 1.8% of reference with a coverageData >= 22X There is a 1.54% of reference with a coverageData >= 23X There is a 1.32% of reference with a coverageData >= 24X There is a 1.13% of reference with a coverageData >= 25X There is a 0.98% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.73% of reference with a coverageData >= 28X There is a 0.64% of reference with a coverageData >= 29X There is a 0.56% of reference with a coverageData >= 30X There is a 0.49% of reference with a coverageData >= 31X There is a 0.43% of reference with a coverageData >= 32X There is a 0.38% of reference with a coverageData >= 33X There is a 0.34% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.27% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.11% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1330851721 5.33941185647036 8.7095159534302 chr2 243199373 1366542232 5.619020374694799 7.3804376579367394 chr3 198022430 1137462402 5.744108897158771 5.346076463537796 chr4 191154276 1062150719 5.5565103811750465 5.999497036897177 chr5 180915260 1000354800 5.529410841296638 5.097263261520253 chr6 171115067 972884049 5.68555455727344 5.773017870174581 chr7 159138663 434134208 2.7280247289748814 3.970723890185717 chr8 146364022 824443203 5.632826918352927 5.460951458415726 chr9 141213431 680639471 4.8199343800378305 6.574247847822568 chr10 135534747 930038037 6.861989693314586 10.0623809296513 chr11 135006516 758861603 5.6209257559094405 5.600654973188153 chr12 133851895 1103318588 8.24283128752118 7.584193099142844 chr13 115169878 501207235 4.351895163073803 4.812762956602988 chr14 107349540 498472137 4.643449212730674 5.2660076947004475 chr15 102531392 464983837 4.5350387615921575 5.311476007672711 chr16 90354753 405283706 4.485471904283774 5.334548820794401 chr17 81195210 373721913 4.602758130682832 5.460832998895849 chr18 78077248 422502324 5.411337295084991 6.52741656000394 chr19 59128983 247055527 4.1782475271052775 6.3827917051109235 chr20 63025520 328147372 5.206579366580395 6.223486439362398 chr21 48129895 196342747 4.079434351560501 8.322513875122524 chr22 51304566 158668085 3.092669861002235 4.624815076199936 chrMT 16571 595644 35.94496409389898 10.346088950294437 chrX 155270560 1066321325 6.867504857327751 6.53361466832899 chrY 59373566 15583472 0.2624648147291675 2.892159293794386