BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779177.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 = 30,587,636 number of mapped reads = 29,569,604 (96.67%) number of supplementary alignments = 172,187 (0.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,936,328 number of mapped paired reads (second in pair) = 14,633,276 number of mapped paired reads (both in pair) = 29,161,790 number of mapped paired reads (singletons) = 407,814 number of mapped bases = 2,952,781,855 bp number of sequenced bases = 2,952,101,555 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,027,948 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 63,976.6298 std insert size = 2,387,515.8262 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.466 >>>>>>> ACTG content number of A's = 898,701,520 bp (30.44%) number of C's = 574,778,823 bp (19.47%) number of T's = 895,593,074 bp (30.34%) number of G's = 581,830,460 bp (19.71%) number of N's = 1,197,678 bp (0.04%) GC percentage = 39.18% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 12,521,989 number of insertions = 246,432 mapped reads with insertion percentage = 0.82% number of deletions = 303,598 mapped reads with deletion percentage = 1.01% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.9538X std coverageData = 2.4156X There is a 36.87% of reference with a coverageData >= 1X There is a 20.82% of reference with a coverageData >= 2X There is a 12.17% of reference with a coverageData >= 3X There is a 7.55% of reference with a coverageData >= 4X There is a 4.87% of reference with a coverageData >= 5X There is a 3.25% of reference with a coverageData >= 6X There is a 2.23% of reference with a coverageData >= 7X There is a 1.57% of reference with a coverageData >= 8X There is a 1.13% of reference with a coverageData >= 9X There is a 0.83% of reference with a coverageData >= 10X There is a 0.62% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% 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 0.03% 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 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% 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 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 205279449 0.8235865097403308 2.6187212087227905 chr2 243199373 171939211 0.7069887100407944 1.964372875762378 chr3 198022430 197386867 0.9967904494455502 1.9168959602521163 chr4 191154276 189744140 0.9926230475744106 1.9165391428287442 chr5 180915260 189480924 1.0473462769254511 1.915374368527047 chr6 171115067 175930124 1.0281392929589304 2.016793820148524 chr7 159138663 251337148 1.579359429455556 5.533058553485142 chr8 146364022 224951056 1.5369286312725132 2.4473399178095554 chr9 141213431 116295003 0.8235406659016733 1.9392099380407428 chr10 135534747 59984248 0.44257468529453925 2.6445219369920627 chr11 135006516 145143254 1.0750833241263704 2.048511025722322 chr12 133851895 163552639 1.2218925925553763 2.2151865239723993 chr13 115169878 84143519 0.7306035263838693 1.692264109943064 chr14 107349540 73193144 0.6818207511648396 1.6211269885584663 chr15 102531392 81634480 0.7961901073185469 1.876326119960181 chr16 90354753 56791555 0.6285397625955549 1.484683801013348 chr17 81195210 54893228 0.6760648565352562 1.7164000666365502 chr18 78077248 79322386 1.0159475139287697 1.976871985996546 chr19 59128983 33434793 0.5654552353792386 1.7580934737217395 chr20 63025520 71948113 1.1415711127809813 2.2525083695697474 chr21 48129895 31267073 0.6496393353860422 1.504469895771009 chr22 51304566 19267568 0.3755526944716772 1.1723840132444998 chrMT 16571 1314 0.07929515418502203 0.4243370423335703 chrX 155270560 273326058 1.7603211967548775 2.9604750001667477 chrY 59373566 2534561 0.042688374149533144 0.5378019631750507