BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781843.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 = 149,806,312 number of mapped reads = 146,201,973 (97.59%) number of supplementary alignments = 532,624 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 73,755,190 number of mapped paired reads (second in pair) = 72,446,783 number of mapped paired reads (both in pair) = 143,824,878 number of mapped paired reads (singletons) = 2,377,095 number of mapped bases = 14,504,228,085 bp number of sequenced bases = 14,501,257,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,502,838 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 44,767.0888 std insert size = 2,102,021.5276 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.9461 >>>>>>> ACTG content number of A's = 4,281,344,892 bp (29.52%) number of C's = 2,957,449,176 bp (20.39%) number of T's = 4,259,186,560 bp (29.37%) number of G's = 3,001,233,670 bp (20.7%) number of N's = 2,043,054 bp (0.01%) GC percentage = 41.09% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 69,578,781 number of insertions = 1,337,464 mapped reads with insertion percentage = 0.9% number of deletions = 1,316,021 mapped reads with deletion percentage = 0.88% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 4.6853X std coverageData = 5.637X There is a 83.02% of reference with a coverageData >= 1X There is a 71.93% of reference with a coverageData >= 2X There is a 60.14% of reference with a coverageData >= 3X There is a 49.14% of reference with a coverageData >= 4X There is a 39.58% of reference with a coverageData >= 5X There is a 31.62% of reference with a coverageData >= 6X There is a 25.17% of reference with a coverageData >= 7X There is a 20.02% of reference with a coverageData >= 8X There is a 15.95% of reference with a coverageData >= 9X There is a 12.73% of reference with a coverageData >= 10X There is a 10.2% of reference with a coverageData >= 11X There is a 8.21% of reference with a coverageData >= 12X There is a 6.64% of reference with a coverageData >= 13X There is a 5.39% of reference with a coverageData >= 14X There is a 4.39% of reference with a coverageData >= 15X There is a 3.6% of reference with a coverageData >= 16X There is a 2.97% of reference with a coverageData >= 17X There is a 2.45% of reference with a coverageData >= 18X There is a 2.04% of reference with a coverageData >= 19X There is a 1.7% of reference with a coverageData >= 20X There is a 1.43% of reference with a coverageData >= 21X There is a 1.2% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 0.87% of reference with a coverageData >= 24X There is a 0.74% of reference with a coverageData >= 25X There is a 0.63% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.47% of reference with a coverageData >= 28X There is a 0.41% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.24% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.12% of reference with a coverageData >= 39X There is a 0.11% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% 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 1653632727 6.63441768114993 9.058940243212728 chr2 243199373 1149127352 4.725042412013126 5.433309390168638 chr3 198022430 954461595 4.819967086556811 4.601437081454318 chr4 191154276 886674924 4.638530419272442 4.913798474780135 chr5 180915260 849550591 4.69584816117778 4.395999659141032 chr6 171115067 819685249 4.790257593155137 4.89232916421532 chr7 159138663 713433005 4.48309035372504 4.916921007564608 chr8 146364022 685652305 4.684568623018572 4.597921008371758 chr9 141213431 566742008 4.013371844212184 5.3434534987374604 chr10 135534747 763741317 5.6350222648071195 7.632692584203936 chr11 135006516 632176400 4.68256213648236 4.772971420644687 chr12 133851895 920738226 6.87878364366825 6.315949817695635 chr13 115169878 429111562 3.725900986019973 4.177038018664078 chr14 107349540 412396285 3.8416213520803164 4.425192608282819 chr15 102531392 388521662 3.789294716685403 4.480338562089584 chr16 90354753 336531931 3.7245625694975892 4.454550823183783 chr17 81195210 308792066 3.8030823000519365 4.650784607498023 chr18 78077248 346533137 4.438336978782859 5.17318639540276 chr19 59128983 202065908 3.4173749952709316 5.199927713396014 chr20 63025520 267707210 4.247600178467389 5.136237758182895 chr21 48129895 160729507 3.339494237417306 6.276162290592285 chr22 51304566 130926943 2.5519549858388824 3.8252310210944573 chrMT 16571 518575 31.29412829642146 10.051998254196084 chrX 155270560 911761519 5.872082376723572 5.663142627779293 chrY 59373566 13016081 0.2192235009094788 2.259221524877082