BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779342.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 = 155,871,204 number of mapped reads = 151,170,143 (96.98%) number of supplementary alignments = 572,248 (0.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 76,246,646 number of mapped paired reads (second in pair) = 74,923,497 number of mapped paired reads (both in pair) = 149,123,730 number of mapped paired reads (singletons) = 2,046,413 number of mapped bases = 14,972,579,993 bp number of sequenced bases = 14,969,327,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,950,578 duplication rate = 6.3% >>>>>>> Insert size mean insert size = 48,194.4511 std insert size = 2,173,767.8422 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.8506 >>>>>>> ACTG content number of A's = 4,409,741,038 bp (29.46%) number of C's = 3,062,625,989 bp (20.46%) number of T's = 4,392,443,104 bp (29.34%) number of G's = 3,103,549,426 bp (20.73%) number of N's = 967,543 bp (0.01%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 53,202,347 number of insertions = 1,430,809 mapped reads with insertion percentage = 0.93% number of deletions = 1,474,319 mapped reads with deletion percentage = 0.96% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 4.8366X std coverageData = 7.108X There is a 83.89% of reference with a coverageData >= 1X There is a 73.69% of reference with a coverageData >= 2X There is a 62.35% of reference with a coverageData >= 3X There is a 51.45% of reference with a coverageData >= 4X There is a 41.72% of reference with a coverageData >= 5X There is a 33.44% of reference with a coverageData >= 6X There is a 26.64% of reference with a coverageData >= 7X There is a 21.15% of reference with a coverageData >= 8X There is a 16.78% of reference with a coverageData >= 9X There is a 13.32% of reference with a coverageData >= 10X There is a 10.6% of reference with a coverageData >= 11X There is a 8.46% of reference with a coverageData >= 12X There is a 6.78% of reference with a coverageData >= 13X There is a 5.46% of reference with a coverageData >= 14X There is a 4.41% of reference with a coverageData >= 15X There is a 3.58% of reference with a coverageData >= 16X There is a 2.92% of reference with a coverageData >= 17X There is a 2.39% of reference with a coverageData >= 18X There is a 1.97% of reference with a coverageData >= 19X There is a 1.63% of reference with a coverageData >= 20X There is a 1.35% of reference with a coverageData >= 21X There is a 1.13% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.8% of reference with a coverageData >= 24X There is a 0.67% of reference with a coverageData >= 25X There is a 0.57% of reference with a coverageData >= 26X There is a 0.49% of reference with a coverageData >= 27X There is a 0.42% of reference with a coverageData >= 28X There is a 0.36% of reference with a coverageData >= 29X There is a 0.31% of reference with a coverageData >= 30X There is a 0.27% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1192108344 4.782769805014849 8.34085306898168 chr2 243199373 1238628596 5.093058344356834 15.59202776744887 chr3 198022430 1015217826 5.126781981212936 4.664804457229673 chr4 191154276 955125500 4.996621158503407 5.341543838587523 chr5 180915260 929342888 5.136896069463681 4.625377061722528 chr6 171115067 880425961 5.145227573677074 5.426143159697295 chr7 159138663 774620315 4.867580890760657 5.2733641112433025 chr8 146364022 744170923 5.0843842143119025 4.791734905808808 chr9 141213431 620372948 4.393158240026049 6.013334267875432 chr10 135534747 837058131 6.175967045557697 7.994356791513459 chr11 135006516 687539892 5.092642284021314 4.955644359528919 chr12 133851895 857039601 6.402894789050241 6.619866252477678 chr13 115169878 455834576 3.9579322641984565 4.268392202488831 chr14 107349540 448587404 4.178754785535178 4.642694389768627 chr15 102531392 422341765 4.119145919719885 4.671968430160818 chr16 90354753 370663790 4.1023164547857265 4.807185718975307 chr17 81195210 348744652 4.295138247687271 5.210891005153638 chr18 78077248 371883671 4.76302226994476 6.062415621639826 chr19 59128983 233504233 3.9490656045952965 6.255267110936632 chr20 63025520 302343141 4.797154247993511 5.3699155076709815 chr21 48129895 178994169 3.7189810823397806 7.294263280596083 chr22 51304566 145845941 2.842747778043771 4.035867585977712 chrMT 16571 4215112 254.36678534789692 58.813938702899485 chrX 155270560 943689354 6.07770947692853 5.640990401572774 chrY 59373566 14281260 0.24053229344520086 2.6324548091557265