BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779161.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 = 25,682,430 number of mapped reads = 24,205,969 (94.25%) number of supplementary alignments = 144,105 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,174,684 number of mapped paired reads (second in pair) = 12,031,285 number of mapped paired reads (both in pair) = 23,942,576 number of mapped paired reads (singletons) = 263,393 number of mapped bases = 2,413,880,063 bp number of sequenced bases = 2,413,327,569 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,306,055 duplication rate = 4.88% >>>>>>> Insert size mean insert size = 54,705.5729 std insert size = 2,252,386.7212 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.5555 >>>>>>> ACTG content number of A's = 741,231,467 bp (30.71%) number of C's = 463,017,718 bp (19.19%) number of T's = 737,203,607 bp (30.55%) number of G's = 470,904,832 bp (19.51%) number of N's = 969,945 bp (0.04%) GC percentage = 38.7% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 9,948,750 number of insertions = 203,372 mapped reads with insertion percentage = 0.83% number of deletions = 249,732 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.7798X std coverageData = 2.7754X There is a 24.69% of reference with a coverageData >= 1X There is a 13.98% of reference with a coverageData >= 2X There is a 8.75% of reference with a coverageData >= 3X There is a 6.04% of reference with a coverageData >= 4X There is a 4.39% of reference with a coverageData >= 5X There is a 3.32% of reference with a coverageData >= 6X There is a 2.57% of reference with a coverageData >= 7X There is a 2.04% of reference with a coverageData >= 8X There is a 1.65% of reference with a coverageData >= 9X There is a 1.35% of reference with a coverageData >= 10X There is a 1.12% of reference with a coverageData >= 11X There is a 0.93% of reference with a coverageData >= 12X There is a 0.79% of reference with a coverageData >= 13X There is a 0.67% of reference with a coverageData >= 14X There is a 0.58% of reference with a coverageData >= 15X There is a 0.5% of reference with a coverageData >= 16X There is a 0.43% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191889167 0.769864348703067 3.2942079986832646 chr2 243199373 190164614 0.7819288826867165 2.551621796133092 chr3 198022430 165297924 0.8347434379024639 2.4867308928100353 chr4 191154276 182822347 0.9564125418779541 2.6258767574971564 chr5 180915260 136165661 0.7526488423364618 2.242457277573016 chr6 171115067 126271969 0.7379360053664941 2.1583623547757718 chr7 159138663 207425448 1.3034258557268388 4.992296334738668 chr8 146364022 185730207 1.268960803769112 3.2450739487567133 chr9 141213431 94917131 0.6721537061159572 2.262190535393158 chr10 135534747 63562301 0.46897421072398504 3.15887937267124 chr11 135006516 110310308 0.8170739551563571 2.760730049017861 chr12 133851895 115381486 0.8620086103375675 2.605790400382639 chr13 115169878 85122977 0.7391079896776481 2.3244271388499995 chr14 107349540 76868188 0.7160551223600958 2.4879357588775184 chr15 102531392 59831847 0.5835466176056597 1.9337487546111058 chr16 90354753 37420296 0.41414861706279027 1.7402255412417007 chr17 81195210 32095163 0.3952839459372049 1.6000878082490426 chr18 78077248 70451840 0.9023350823020811 2.5707615717136627 chr19 59128983 18947803 0.3204486537507334 1.6472536354711405 chr20 63025520 53600171 0.8504518645780312 2.6912688989274116 chr21 48129895 27671281 0.5749291786321162 2.404726738277504 chr22 51304566 16950325 0.33038628569628675 1.9581442945254557 chrMT 16571 3794 0.22895419709130407 0.70616088344208 chrX 155270560 163154650 1.050776463999357 3.417952013323418 chrY 59373566 1823165 0.030706678456874227 0.46909222399945993