BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779319.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 = 19,292,916 number of mapped reads = 18,141,959 (94.03%) number of supplementary alignments = 46,952 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,128,029 number of mapped paired reads (second in pair) = 9,013,930 number of mapped paired reads (both in pair) = 17,995,430 number of mapped paired reads (singletons) = 146,529 number of mapped bases = 1,444,214,931 bp number of sequenced bases = 1,443,936,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 620,966 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 33,788.7873 std insert size = 1,749,024.3875 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.1025 >>>>>>> ACTG content number of A's = 442,979,731 bp (30.68%) number of C's = 276,919,050 bp (19.18%) number of T's = 441,763,015 bp (30.59%) number of G's = 281,886,948 bp (19.52%) number of N's = 387,873 bp (0.03%) GC percentage = 38.7% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,961,996 number of insertions = 106,408 mapped reads with insertion percentage = 0.58% number of deletions = 134,179 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.4665X std coverageData = 1.6891X There is a 19.36% of reference with a coverageData >= 1X There is a 9.2% of reference with a coverageData >= 2X There is a 5.18% of reference with a coverageData >= 3X There is a 3.26% of reference with a coverageData >= 4X There is a 2.2% of reference with a coverageData >= 5X There is a 1.55% of reference with a coverageData >= 6X There is a 1.13% of reference with a coverageData >= 7X There is a 0.85% of reference with a coverageData >= 8X There is a 0.65% of reference with a coverageData >= 9X There is a 0.51% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 115187809 0.46213649754557684 1.9831853664795553 chr2 243199373 114091675 0.4691281625960442 1.4437006828283216 chr3 198022430 99141832 0.5006596070960244 1.55254556552123 chr4 191154276 109186007 0.5711931183794183 1.634170643174028 chr5 180915260 81378852 0.4498175112480838 1.4042508990771 chr6 171115067 75111775 0.43895477070993405 1.3421717963865842 chr7 159138663 124212934 0.7805327232138427 3.0382893246609375 chr8 146364022 111051788 0.7587369251167476 2.013825622274358 chr9 141213431 56649653 0.40116334968166023 1.3906326679654315 chr10 135534747 38001364 0.28038097123536887 1.781993530582185 chr11 135006516 66042111 0.48917721126882496 1.711955926114924 chr12 133851895 68952321 0.5151389227623561 1.5983595713490675 chr13 115169878 51135348 0.4439993241982943 1.4402429933273349 chr14 107349540 45783979 0.42649441255174453 1.5294499521077294 chr15 102531392 35903192 0.35016780031621925 1.184841945534358 chr16 90354753 22409394 0.24801566332653247 1.0862039811438087 chr17 81195210 19110535 0.23536530049001658 0.9456816450818233 chr18 78077248 42116565 0.5394217403769149 1.6112392810403366 chr19 59128983 11427103 0.19325722209698754 1.0820459255574186 chr20 63025520 32247944 0.5116648621066514 1.6657189494120501 chr21 48129895 16667702 0.34630663540820106 1.500690374936736 chr22 51304566 10226349 0.19932629388191297 1.195594533094188 chrMT 16571 2468 0.1489348862470581 0.52102200047012 chrX 155270560 97041964 0.624986243367706 2.079210687423503 chrY 59373566 1134267 0.01910390560001062 0.25358905601402926