BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779081.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 = 22,903,382 number of mapped reads = 22,097,234 (96.48%) number of supplementary alignments = 122,323 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,131,788 number of mapped paired reads (second in pair) = 10,965,446 number of mapped paired reads (both in pair) = 21,844,234 number of mapped paired reads (singletons) = 253,000 number of mapped bases = 2,203,613,994 bp number of sequenced bases = 2,203,101,981 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 812,303 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 62,064.6664 std insert size = 2,388,414.1392 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.4798 >>>>>>> ACTG content number of A's = 674,058,430 bp (30.6%) number of C's = 425,310,037 bp (19.31%) number of T's = 670,922,800 bp (30.45%) number of G's = 432,067,569 bp (19.61%) number of N's = 743,145 bp (0.03%) GC percentage = 38.92% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 10,205,022 number of insertions = 189,156 mapped reads with insertion percentage = 0.84% number of deletions = 230,738 mapped reads with deletion percentage = 1.02% homopolymer indels = 46.47% >>>>>>> Coverage mean coverageData = 0.7118X std coverageData = 2.1966X There is a 28.27% of reference with a coverageData >= 1X There is a 15.47% of reference with a coverageData >= 2X There is a 8.9% of reference with a coverageData >= 3X There is a 5.52% of reference with a coverageData >= 4X There is a 3.57% of reference with a coverageData >= 5X There is a 2.38% of reference with a coverageData >= 6X There is a 1.64% of reference with a coverageData >= 7X There is a 1.16% of reference with a coverageData >= 8X There is a 0.83% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% 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 0.02% 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 0.01% 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 191029195 0.7664141185830787 3.249957011032046 chr2 243199373 175654932 0.7222672074898812 1.8137674520681355 chr3 198022430 117325804 0.5924874470028471 1.5272625595453224 chr4 191154276 156659904 0.8195469506525713 1.901032237720113 chr5 180915260 126327283 0.6982677027907983 1.6361779006099635 chr6 171115067 117339625 0.6857352017984483 1.6314889749729333 chr7 159138663 198367998 1.2465103970365767 4.167751519366853 chr8 146364022 212844227 1.4542113839970865 2.5052373443701303 chr9 141213431 82164592 0.5818468641272515 1.6765453807746395 chr10 135534747 67440796 0.4975904518418439 3.6843707093568 chr11 135006516 84159350 0.6233725044797097 1.5369969263752776 chr12 133851895 125300492 0.9361129478219191 1.9517993872835284 chr13 115169878 39192981 0.3403058306617291 1.0675860187398936 chr14 107349540 55271323 0.5148724717404471 1.4478960009950415 chr15 102531392 61616180 0.6009494145948979 1.6104847809672027 chr16 90354753 43390430 0.48022299391377893 1.2896044962833424 chr17 81195210 43786448 0.5392737822834622 1.5406755247206656 chr18 78077248 68015882 0.8711357500715189 1.9759238928804497 chr19 59128983 25265255 0.4272905387193959 2.0937919845448154 chr20 63025520 46077318 0.7310898505875081 1.675877212339246 chr21 48129895 30096030 0.625308449145796 1.509150475836389 chr22 51304566 9494230 0.18505623846423339 0.7248520215174036 chrMT 16571 3174 0.19153943636473358 0.545232576875925 chrX 155270560 125208187 0.8063871670199425 1.9397588010556166 chrY 59373566 1582358 0.026650883660920752 0.3747099845619691