BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779400.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 = 18,206,876 number of mapped reads = 17,398,072 (95.56%) number of supplementary alignments = 59,483 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,766,848 number of mapped paired reads (second in pair) = 8,631,224 number of mapped paired reads (both in pair) = 17,227,090 number of mapped paired reads (singletons) = 170,982 number of mapped bases = 1,382,823,064 bp number of sequenced bases = 1,382,514,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 697,679 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 47,050.9148 std insert size = 2,046,419.4689 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.4118 >>>>>>> ACTG content number of A's = 414,390,304 bp (29.97%) number of C's = 275,371,605 bp (19.92%) number of T's = 412,272,268 bp (29.82%) number of G's = 280,177,007 bp (20.27%) number of N's = 303,744 bp (0.02%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 4,624,412 number of insertions = 124,792 mapped reads with insertion percentage = 0.71% number of deletions = 147,685 mapped reads with deletion percentage = 0.84% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.4467X std coverageData = 1.8582X There is a 22.54% of reference with a coverageData >= 1X There is a 9.75% of reference with a coverageData >= 2X There is a 4.45% of reference with a coverageData >= 3X There is a 2.22% of reference with a coverageData >= 4X There is a 1.2% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.24% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 85294615 0.3422042226326088 3.726127606955847 chr2 243199373 108596020 0.4465308387123186 1.1075659873484511 chr3 198022430 72702386 0.36714217677260097 0.9008629002648074 chr4 191154276 58641606 0.3067763234341669 0.8083500216788976 chr5 180915260 133094474 0.7356730106680884 1.309608236575789 chr6 171115067 93096458 0.5440576311143892 2.2113882204404196 chr7 159138663 150945043 0.9485127005245734 2.6777448702868845 chr8 146364022 63184941 0.43169721723006493 1.0044243649589901 chr9 141213431 138480507 0.9806468550431298 4.074575617500501 chr10 135534747 40668184 0.3000572539527447 1.610274697607203 chr11 135006516 57720646 0.42753970482432124 1.1150436495312472 chr12 133851895 63262322 0.4726292593765669 1.0300798832721278 chr13 115169878 41631849 0.3614820969073181 0.9035878772870893 chr14 107349540 38542698 0.3590392469311 0.8848317126747459 chr15 102531392 31693710 0.3091122570539177 0.8403001573800163 chr16 90354753 20690176 0.2289882414929517 0.7502124615703256 chr17 81195210 35209853 0.4336444600611292 1.0794556820557053 chr18 78077248 42760242 0.5476658449847003 1.4761399722607094 chr19 59128983 17679897 0.29900559933527016 2.2170750033148967 chr20 63025520 22068158 0.3501463851468421 0.9211091199624636 chr21 48129895 17507188 0.36374872623345633 0.9457293588408732 chr22 51304566 13128902 0.25590123888778243 0.7765851242704095 chrMT 16571 1102 0.06650171987206566 0.2850778711081544 chrX 155270560 31288276 0.2015081030170819 0.6684254978992453 chrY 59373566 4933811 0.08309777115290666 0.4543101459145431