BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779313.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 = 17,105,644 number of mapped reads = 15,862,535 (92.73%) number of supplementary alignments = 41,764 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,014,817 number of mapped paired reads (second in pair) = 7,847,718 number of mapped paired reads (both in pair) = 15,662,502 number of mapped paired reads (singletons) = 200,033 number of mapped bases = 1,262,734,420 bp number of sequenced bases = 1,262,496,374 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 361,638 duplication rate = 2.09% >>>>>>> Insert size mean insert size = 41,569.7878 std insert size = 1,945,756.4169 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 53.0892 >>>>>>> ACTG content number of A's = 388,999,053 bp (30.81%) number of C's = 240,404,019 bp (19.04%) number of T's = 388,083,099 bp (30.74%) number of G's = 244,673,055 bp (19.38%) number of N's = 337,148 bp (0.03%) GC percentage = 38.42% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 4,404,981 number of insertions = 91,134 mapped reads with insertion percentage = 0.57% number of deletions = 116,131 mapped reads with deletion percentage = 0.72% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.4079X std coverageData = 1.308X There is a 20.25% of reference with a coverageData >= 1X There is a 8.51% of reference with a coverageData >= 2X There is a 4.3% of reference with a coverageData >= 3X There is a 2.45% of reference with a coverageData >= 4X There is a 1.51% of reference with a coverageData >= 5X There is a 0.99% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.19% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% 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 93579847 0.3754447897644355 1.4104051330978156 chr2 243199373 109772028 0.4513664103895531 1.2666724776721947 chr3 198022430 105385376 0.5321890858525471 1.4599433003545979 chr4 191154276 97082233 0.5078737187129416 1.3388485629381344 chr5 180915260 81670178 0.45142780106001007 1.3464433208560618 chr6 171115067 85219414 0.4980240226303391 1.333917148653555 chr7 159138663 71404693 0.44869481528822447 1.3186825698707123 chr8 146364022 75936299 0.5188180671886702 1.3461182138701444 chr9 141213431 47486430 0.33627417494020095 1.1166560894485844 chr10 135534747 47231370 0.3484816332744547 2.043633757684558 chr11 135006516 55354677 0.41001485439413904 1.1917276072306704 chr12 133851895 67064392 0.5010343110943629 1.4481269128165544 chr13 115169878 41033016 0.3562825342230544 1.0296447750186588 chr14 107349540 36775549 0.3425776114178039 1.149600748520566 chr15 102531392 31888306 0.311010173352567 1.0997698898756059 chr16 90354753 20543600 0.22736601360638992 0.803500859797742 chr17 81195210 18078168 0.2226506711418075 0.8652898933957445 chr18 78077248 31748862 0.4066339786976098 1.2106188697506466 chr19 59128983 10520519 0.1779249103607955 0.9523493114652918 chr20 63025520 20523090 0.3256314267617308 1.0468199653101136 chr21 48129895 14225744 0.29556981165240437 0.9094736737453938 chr22 51304566 5941173 0.11580203212322272 0.5233361753218768 chrMT 16571 952 0.057449761631766336 0.2554467106103607 chrX 155270560 93439742 0.6017865975365839 1.6320995098660207 chrY 59373566 828762 0.013958433960325037 0.18572223168883745