BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779097.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 = 16,219,998 number of mapped reads = 15,776,913 (97.27%) number of supplementary alignments = 87,078 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,939,989 number of mapped paired reads (second in pair) = 7,836,924 number of mapped paired reads (both in pair) = 15,616,606 number of mapped paired reads (singletons) = 160,307 number of mapped bases = 1,576,323,799 bp number of sequenced bases = 1,575,952,089 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 380,590 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 64,258.9516 std insert size = 2,442,827.0295 median insert size = 217 >>>>>>> Mapping quality mean mapping quality = 53.4258 >>>>>>> ACTG content number of A's = 485,197,851 bp (30.79%) number of C's = 301,144,336 bp (19.11%) number of T's = 483,126,159 bp (30.66%) number of G's = 305,849,203 bp (19.41%) number of N's = 634,540 bp (0.04%) GC percentage = 38.52% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 6,639,828 number of insertions = 135,225 mapped reads with insertion percentage = 0.84% number of deletions = 165,969 mapped reads with deletion percentage = 1.03% homopolymer indels = 46.77% >>>>>>> Coverage mean coverageData = 0.5092X std coverageData = 1.4608X There is a 24.6% of reference with a coverageData >= 1X There is a 11.56% of reference with a coverageData >= 2X There is a 5.81% of reference with a coverageData >= 3X There is a 3.19% of reference with a coverageData >= 4X There is a 1.85% of reference with a coverageData >= 5X There is a 1.13% of reference with a coverageData >= 6X There is a 0.71% of reference with a coverageData >= 7X There is a 0.47% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% 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 0.02% 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 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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% 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 57772585 0.23178511960457662 1.3729603756045774 chr2 243199373 171184930 0.7038872176697594 1.5998340738545418 chr3 198022430 124537803 0.628907558603336 1.3698473119807364 chr4 191154276 142309025 0.7444720985472488 1.4530068097175843 chr5 180915260 105004432 0.5804067163820232 1.291521423097669 chr6 171115067 38630034 0.2257547197757869 0.7569756349784846 chr7 159138663 154742603 0.9723759147077916 2.903927795134812 chr8 146364022 105263595 0.7191903690648785 1.4337383960904626 chr9 141213431 59711168 0.42284340502993656 1.1956756004630338 chr10 135534747 37202216 0.27448471202738883 1.942349662205016 chr11 135006516 83395750 0.6177164811808047 1.430469003219494 chr12 133851895 68456879 0.5114375033689288 1.2646324317448463 chr13 115169878 56318788 0.48900623129947224 1.2265660125545477 chr14 107349540 56052157 0.5221462243806541 1.244481534435479 chr15 102531392 37768603 0.3683613600018227 1.0454094810355696 chr16 90354753 24914580 0.2757417753109236 0.8498840171122592 chr17 81195210 20107746 0.2476469486315757 0.9676208550381532 chr18 78077248 47857688 0.6129530590012598 1.3592684853047043 chr19 59128983 14311691 0.24204189339769297 1.0005154486635974 chr20 63025520 31353048 0.49746591539427204 1.285849880057629 chr21 48129895 17302088 0.35948734149534295 1.0886652126978786 chr22 51304566 6417473 0.1250858062029021 0.5575302291533779 chrMT 16571 844 0.05093235169875083 0.23804631656520323 chrX 155270560 114646415 0.7383654377236741 1.5189451565221888 chrY 59373566 1061658 0.017880987643558416 0.2899311366360121