BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779396.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 = 15,123,846 number of mapped reads = 12,271,614 (81.14%) number of supplementary alignments = 48,012 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,178,241 number of mapped paired reads (second in pair) = 6,093,373 number of mapped paired reads (both in pair) = 12,112,002 number of mapped paired reads (singletons) = 159,612 number of mapped bases = 971,805,922 bp number of sequenced bases = 971,558,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 978,366 duplication rate = 6.87% >>>>>>> Insert size mean insert size = 62,477.06 std insert size = 2,603,589.1046 median insert size = 158 >>>>>>> Mapping quality mean mapping quality = 49.2752 >>>>>>> ACTG content number of A's = 284,525,475 bp (29.29%) number of C's = 199,588,578 bp (20.54%) number of T's = 283,413,325 bp (29.17%) number of G's = 203,815,725 bp (20.98%) number of N's = 215,261 bp (0.02%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 3,539,006 number of insertions = 97,436 mapped reads with insertion percentage = 0.79% number of deletions = 115,698 mapped reads with deletion percentage = 0.93% homopolymer indels = 46.49% >>>>>>> Coverage mean coverageData = 0.3139X std coverageData = 2.5215X There is a 8.64% of reference with a coverageData >= 1X There is a 5.06% of reference with a coverageData >= 2X There is a 3.34% of reference with a coverageData >= 3X There is a 2.45% of reference with a coverageData >= 4X There is a 1.88% of reference with a coverageData >= 5X There is a 1.49% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.68% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.31% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.2% of reference with a coverageData >= 18X There is a 0.18% of reference with a coverageData >= 19X There is a 0.16% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.04% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% 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 204792557 0.8216330863223807 5.7580869897887315 chr2 243199373 19741250 0.0811731122349563 1.0602847869054963 chr3 198022430 31429188 0.15871529300998882 2.23495330952227 chr4 191154276 22296667 0.11664226124870991 0.901643022477765 chr5 180915260 214255252 1.1842851288498273 3.6092712162760523 chr6 171115067 13682291 0.07995959233677534 0.7622314793800138 chr7 159138663 105780625 0.664707262244625 3.8601566290526863 chr8 146364022 34880498 0.23831333358685647 1.1777613911460678 chr9 141213431 9977335 0.07065429208359084 0.8238196368568017 chr10 135534747 16481719 0.1216051187228025 3.0215502424161285 chr11 135006516 143755856 1.064806797917813 3.6125167391492248 chr12 133851895 33895105 0.25322842833117903 1.1860000115714282 chr13 115169878 20216930 0.17554008349301195 1.107167689277876 chr14 107349540 6127806 0.057082741109090916 0.44323386601124654 chr15 102531392 20462294 0.19957101528476273 1.13915313553155 chr16 90354753 14956488 0.16553072753128992 1.1827603880536477 chr17 81195210 11776540 0.1450398367095793 0.8202100629691781 chr18 78077248 13538057 0.17339311190886236 1.12005094737571 chr19 59128983 5525394 0.0934464575519589 3.016415882466487 chr20 63025520 5724773 0.09083261827907171 0.7594198375903096 chr21 48129895 12207266 0.25363167735977815 1.3975714380952042 chr22 51304566 3375143 0.06578640583374197 0.5027519670286182 chrMT 16571 400 0.024138555307464848 0.17025586744459908 chrX 155270560 4493780 0.028941610051512662 0.4605724640234672 chrY 59373566 2432708 0.040972913771087964 0.36843789834188645