BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778040.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 = 193,952,890 number of mapped reads = 181,564,854 (93.61%) number of supplementary alignments = 229,853 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 91,632,028 number of mapped paired reads (second in pair) = 89,932,826 number of mapped paired reads (both in pair) = 178,991,988 number of mapped paired reads (singletons) = 2,572,866 number of mapped bases = 12,580,024,332 bp number of sequenced bases = 12,578,754,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,734,637 duplication rate = 40.97% >>>>>>> Insert size mean insert size = 23,008.8607 std insert size = 1,485,655.6574 median insert size = 103 >>>>>>> Mapping quality mean mapping quality = 51.9022 >>>>>>> ACTG content number of A's = 3,187,563,292 bp (25.34%) number of C's = 3,112,775,897 bp (24.75%) number of T's = 3,184,501,022 bp (25.32%) number of G's = 3,092,411,610 bp (24.58%) number of N's = 1,502,505 bp (0.01%) GC percentage = 49.33% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 65,018,852 number of insertions = 432,961 mapped reads with insertion percentage = 0.24% number of deletions = 579,866 mapped reads with deletion percentage = 0.31% homopolymer indels = 36.72% >>>>>>> Coverage mean coverageData = 4.0637X std coverageData = 40.2608X There is a 41.78% of reference with a coverageData >= 1X There is a 27.95% of reference with a coverageData >= 2X There is a 16.44% of reference with a coverageData >= 3X There is a 11.95% of reference with a coverageData >= 4X There is a 8.1% of reference with a coverageData >= 5X There is a 6.32% of reference with a coverageData >= 6X There is a 4.87% of reference with a coverageData >= 7X There is a 4.1% of reference with a coverageData >= 8X There is a 3.49% of reference with a coverageData >= 9X There is a 3.13% of reference with a coverageData >= 10X There is a 2.85% of reference with a coverageData >= 11X There is a 2.67% of reference with a coverageData >= 12X There is a 2.52% of reference with a coverageData >= 13X There is a 2.41% of reference with a coverageData >= 14X There is a 2.32% of reference with a coverageData >= 15X There is a 2.24% of reference with a coverageData >= 16X There is a 2.18% of reference with a coverageData >= 17X There is a 2.13% of reference with a coverageData >= 18X There is a 2.08% of reference with a coverageData >= 19X There is a 2.04% of reference with a coverageData >= 20X There is a 2.01% of reference with a coverageData >= 21X There is a 1.97% of reference with a coverageData >= 22X There is a 1.94% of reference with a coverageData >= 23X There is a 1.91% of reference with a coverageData >= 24X There is a 1.88% of reference with a coverageData >= 25X There is a 1.86% of reference with a coverageData >= 26X There is a 1.83% of reference with a coverageData >= 27X There is a 1.81% of reference with a coverageData >= 28X There is a 1.79% of reference with a coverageData >= 29X There is a 1.76% of reference with a coverageData >= 30X There is a 1.74% of reference with a coverageData >= 31X There is a 1.72% of reference with a coverageData >= 32X There is a 1.7% of reference with a coverageData >= 33X There is a 1.68% of reference with a coverageData >= 34X There is a 1.67% of reference with a coverageData >= 35X There is a 1.65% of reference with a coverageData >= 36X There is a 1.63% of reference with a coverageData >= 37X There is a 1.61% of reference with a coverageData >= 38X There is a 1.6% of reference with a coverageData >= 39X There is a 1.58% of reference with a coverageData >= 40X There is a 1.56% of reference with a coverageData >= 41X There is a 1.55% of reference with a coverageData >= 42X There is a 1.53% of reference with a coverageData >= 43X There is a 1.52% of reference with a coverageData >= 44X There is a 1.5% of reference with a coverageData >= 45X There is a 1.49% of reference with a coverageData >= 46X There is a 1.48% of reference with a coverageData >= 47X There is a 1.46% of reference with a coverageData >= 48X There is a 1.45% of reference with a coverageData >= 49X There is a 1.44% of reference with a coverageData >= 50X There is a 1.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1267357111 5.084669823149608 48.4680867003084 chr2 243199373 884097047 3.6352768351915117 31.676678890333026 chr3 198022430 663587987 3.3510748605599883 31.9719894604932 chr4 191154276 514835276 2.693297198332095 23.694263418455687 chr5 180915260 560916022 3.100435098730754 24.3598523118813 chr6 171115067 574786404 3.359063664452178 28.15645021523737 chr7 159138663 1051254425 6.605902080501958 100.18537166491126 chr8 146364022 610415615 4.17053048050292 33.63745308187223 chr9 141213431 473267757 3.351435863066028 28.0456781607305 chr10 135534747 295888145 2.1831165184526444 28.430860901566305 chr11 135006516 634443690 4.6993560666360725 34.47731647364056 chr12 133851895 569388109 4.253866626243879 29.98362428258907 chr13 115169878 231006234 2.005786912442505 19.93756412740176 chr14 107349540 382454637 3.5627040134498946 29.94863522564619 chr15 102531392 424567172 4.1408505601874595 32.76790327580444 chr16 90354753 489510530 5.417651133416302 36.93069875826514 chr17 81195210 615914219 7.585597955840006 50.38911234718322 chr18 78077248 205664746 2.6341187896376677 23.911977908012936 chr19 59128983 764973579 12.93737081525654 67.16291844379735 chr20 63025520 392823561 6.232769852593045 40.87709728697708 chr21 48129895 137324229 2.853200261500674 26.820263940518046 chr22 51304566 230191314 4.486760769012255 31.01699638207031 chrMT 16571 670379 40.454951421157446 18.826527590103833 chrX 155270560 582448345 3.7511833859554575 40.329642142765316 chrY 59373566 22237799 0.37454039732092226 20.97300589314299