BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1778448.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 = 341,794,014 number of mapped reads = 329,845,406 (96.5%) number of supplementary alignments = 843,792 (0.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 166,085,396 number of mapped paired reads (second in pair) = 163,760,010 number of mapped paired reads (both in pair) = 325,633,970 number of mapped paired reads (singletons) = 4,211,436 number of mapped bases = 26,089,169,439 bp number of sequenced bases = 26,082,184,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,943,985 duplication rate = 8.82% >>>>>>> Insert size mean insert size = 68,317.6741 std insert size = 2,485,439.9927 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 53.0047 >>>>>>> ACTG content number of A's = 7,769,336,999 bp (29.79%) number of C's = 5,284,137,309 bp (20.26%) number of T's = 7,698,889,919 bp (29.52%) number of G's = 5,322,511,251 bp (20.41%) number of N's = 7,309,188 bp (0.03%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 130,112,848 number of insertions = 2,451,411 mapped reads with insertion percentage = 0.73% number of deletions = 3,172,582 mapped reads with deletion percentage = 0.94% homopolymer indels = 43% >>>>>>> Coverage mean coverageData = 8.4276X std coverageData = 95.9098X There is a 91.93% of reference with a coverageData >= 1X There is a 90.53% of reference with a coverageData >= 2X There is a 87.66% of reference with a coverageData >= 3X There is a 83% of reference with a coverageData >= 4X There is a 76.57% of reference with a coverageData >= 5X There is a 68.58% of reference with a coverageData >= 6X There is a 59.49% of reference with a coverageData >= 7X There is a 49.93% of reference with a coverageData >= 8X There is a 40.56% of reference with a coverageData >= 9X There is a 31.99% of reference with a coverageData >= 10X There is a 24.62% of reference with a coverageData >= 11X There is a 18.6% of reference with a coverageData >= 12X There is a 13.9% of reference with a coverageData >= 13X There is a 10.34% of reference with a coverageData >= 14X There is a 7.7% of reference with a coverageData >= 15X There is a 5.76% of reference with a coverageData >= 16X There is a 4.35% of reference with a coverageData >= 17X There is a 3.3% of reference with a coverageData >= 18X There is a 2.53% of reference with a coverageData >= 19X There is a 1.96% of reference with a coverageData >= 20X There is a 1.53% of reference with a coverageData >= 21X There is a 1.21% of reference with a coverageData >= 22X There is a 0.98% of reference with a coverageData >= 23X There is a 0.81% of reference with a coverageData >= 24X There is a 0.69% of reference with a coverageData >= 25X There is a 0.61% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.5% of reference with a coverageData >= 28X There is a 0.47% of reference with a coverageData >= 29X There is a 0.45% of reference with a coverageData >= 30X There is a 0.43% of reference with a coverageData >= 31X There is a 0.41% of reference with a coverageData >= 32X There is a 0.4% of reference with a coverageData >= 33X There is a 0.39% of reference with a coverageData >= 34X There is a 0.39% of reference with a coverageData >= 35X There is a 0.38% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.37% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.35% of reference with a coverageData >= 41X There is a 0.35% of reference with a coverageData >= 42X There is a 0.34% of reference with a coverageData >= 43X There is a 0.34% of reference with a coverageData >= 44X There is a 0.33% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.33% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.32% of reference with a coverageData >= 49X There is a 0.32% of reference with a coverageData >= 50X There is a 0.31% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2070766909 8.307970911735461 245.75050918520415 chr2 243199373 2151804489 8.847903111164682 56.574069720971664 chr3 198022430 1657997540 8.372776457697242 11.856365356272532 chr4 191154276 1651450891 8.639361491447882 51.705256753658816 chr5 180915260 2140095824 11.829272024924819 9.099083050792585 chr6 171115067 1180773890 6.900467099136279 28.317103252930224 chr7 159138663 2800015272 17.594814605172346 135.52045317731896 chr8 146364022 1264717805 8.640906335574735 91.72794607538223 chr9 141213431 1285406999 9.102583160096152 70.05157553882204 chr10 135534747 883852641 6.521225446342553 179.14221077907382 chr11 135006516 1142213387 8.460431546874375 43.005267366599334 chr12 133851895 1105455403 8.258795312535545 8.494579765435525 chr13 115169878 796220240 6.913441724753759 5.355069847587179 chr14 107349540 713336191 6.644986005529227 9.839340363574657 chr15 102531392 577860631 5.635938610879291 5.035343383665518 chr16 90354753 689395453 7.629874800277524 36.28278886516301 chr17 81195210 689877972 8.496535349806965 37.42248394564223 chr18 78077248 671063984 8.594872401240371 97.07124857664031 chr19 59128983 507386125 8.581005443641741 130.9244850915268 chr20 63025520 512730067 8.135277059197607 14.61241925937065 chr21 48129895 349309828 7.257647829898652 34.691225815634915 chr22 51304566 300132530 5.850015961542292 22.282121676564504 chrMT 16571 20733866 1251.2139279464125 119.43758266305748 chrX 155270560 672228055 4.329398019817794 17.559056137717416 chrY 59373566 254343447 4.283782567481293 71.90195270991819