BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1768995.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 = 378,276,896 number of mapped reads = 340,669,333 (90.06%) number of supplementary alignments = 305,113 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 172,464,508 number of mapped paired reads (second in pair) = 168,204,825 number of mapped paired reads (both in pair) = 334,153,546 number of mapped paired reads (singletons) = 6,515,787 number of mapped bases = 27,006,914,578 bp number of sequenced bases = 27,000,260,675 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,837,693 duplication rate = 7.15% >>>>>>> Insert size mean insert size = 29,890.4772 std insert size = 1,646,635.1388 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.1925 >>>>>>> ACTG content number of A's = 7,806,347,722 bp (28.91%) number of C's = 5,665,562,825 bp (20.98%) number of T's = 7,846,012,896 bp (29.06%) number of G's = 5,674,975,705 bp (21.02%) number of N's = 7,361,527 bp (0.03%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 130,885,295 number of insertions = 2,336,617 mapped reads with insertion percentage = 0.67% number of deletions = 3,063,720 mapped reads with deletion percentage = 0.88% homopolymer indels = 43.84% >>>>>>> Coverage mean coverageData = 8.724X std coverageData = 83.8561X There is a 91.55% of reference with a coverageData >= 1X There is a 90.86% of reference with a coverageData >= 2X There is a 89.23% of reference with a coverageData >= 3X There is a 86.11% of reference with a coverageData >= 4X There is a 81.13% of reference with a coverageData >= 5X There is a 74.2% of reference with a coverageData >= 6X There is a 65.61% of reference with a coverageData >= 7X There is a 55.98% of reference with a coverageData >= 8X There is a 46.09% of reference with a coverageData >= 9X There is a 36.67% of reference with a coverageData >= 10X There is a 28.28% of reference with a coverageData >= 11X There is a 21.23% of reference with a coverageData >= 12X There is a 15.57% of reference with a coverageData >= 13X There is a 11.21% of reference with a coverageData >= 14X There is a 7.96% of reference with a coverageData >= 15X There is a 5.6% of reference with a coverageData >= 16X There is a 3.92% of reference with a coverageData >= 17X There is a 2.74% of reference with a coverageData >= 18X There is a 1.93% of reference with a coverageData >= 19X There is a 1.37% of reference with a coverageData >= 20X There is a 0.99% of reference with a coverageData >= 21X There is a 0.74% of reference with a coverageData >= 22X There is a 0.57% of reference with a coverageData >= 23X There is a 0.46% of reference with a coverageData >= 24X There is a 0.38% of reference with a coverageData >= 25X There is a 0.33% of reference with a coverageData >= 26X There is a 0.3% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.12% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2106911421 8.452983637701749 226.00964691776144 chr2 243199373 2189353329 9.002298410530853 63.13860992858689 chr3 198022430 1656446856 8.36494560742437 6.813657461358962 chr4 191154276 1618925108 8.46920687246358 39.110683595655416 chr5 180915260 1516522248 8.382500447999798 6.995944002852714 chr6 171115067 1366449391 7.985558577375305 29.792740832619145 chr7 159138663 2493874965 15.671081546035108 107.11550317216718 chr8 146364022 1825083718 12.469483231336728 76.03610408845634 chr9 141213431 1038611371 7.354905009000171 73.66916029533034 chr10 135534747 766721823 5.657012979852317 121.70695150939474 chr11 135006516 1175423904 8.70642350329224 29.067012065231552 chr12 133851895 1125172469 8.406100406721922 7.660682570569841 chr13 115169878 777833583 6.753793583075603 5.8479587201111665 chr14 107349540 775720382 7.226117429101233 10.77193347663139 chr15 102531392 732642109 7.145539475363798 5.503724450388201 chr16 90354753 820990949 9.086306162554614 44.923862107927164 chr17 81195210 747742248 9.209191625959216 42.23626194968738 chr18 78077248 688172032 8.813989345526112 91.02432677270535 chr19 59128983 743616149 12.576170116100254 117.86385969474749 chr20 63025520 806591989 12.797863294106895 12.573471143642585 chr21 48129895 346614553 7.201647811614798 20.71336008285661 chr22 51304566 332328721 6.477566168282176 6.674382726208576 chrMT 16571 5534047 333.9597489590248 39.99662731121943 chrX 155270560 1275086628 8.21203084473966 18.156088948832018 chrY 59373566 74544585 1.2555180701122113 44.535000987292506