BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173909.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,887,734 number of mapped reads = 4,764,523 (97.48%) number of supplementary alignments = 466,295 (9.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,387,401 number of mapped paired reads (second in pair) = 2,377,122 number of mapped paired reads (both in pair) = 4,682,050 number of mapped paired reads (singletons) = 82,473 number of mapped bases = 561,938,657 bp number of sequenced bases = 561,634,790 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,538,863 duplication rate = 62.83% >>>>>>> Insert size mean insert size = 717,033.8896 std insert size = 7,603,590.4502 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.7871 >>>>>>> ACTG content number of A's = 170,698,999 bp (30.39%) number of C's = 108,577,946 bp (19.33%) number of T's = 170,314,501 bp (30.32%) number of G's = 112,036,558 bp (19.95%) number of N's = 6,786 bp (0%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 5,585,115 number of insertions = 57,781 mapped reads with insertion percentage = 1.17% number of deletions = 123,682 mapped reads with deletion percentage = 2.53% homopolymer indels = 43.55% >>>>>>> Coverage mean coverageData = 0.1815X std coverageData = 2.648X There is a 4.17% of reference with a coverageData >= 1X There is a 3.19% of reference with a coverageData >= 2X There is a 2.34% of reference with a coverageData >= 3X There is a 1.88% of reference with a coverageData >= 4X There is a 1.37% of reference with a coverageData >= 5X There is a 1.1% of reference with a coverageData >= 6X There is a 0.79% of reference with a coverageData >= 7X There is a 0.65% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.02% 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% 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 50962303 0.20446209038732946 1.5443711186635527 chr2 243199373 41160907 0.16924758683485586 7.676311646747163 chr3 198022430 35323180 0.17837969163392248 1.1735651034306978 chr4 191154276 34466114 0.1803052211084203 1.4372355740071496 chr5 180915260 28652282 0.1583740476065977 1.0888803469534538 chr6 171115067 27746071 0.1621486143005747 1.149620470180914 chr7 159138663 49578165 0.31154066563949956 2.8634799293123434 chr8 146364022 55728087 0.38074990177572465 2.06392662301209 chr9 141213431 19748340 0.13984746252642216 1.3083015506175395 chr10 135534747 25108637 0.1852560878724332 3.32780340151727 chr11 135006516 23278480 0.1724248628118068 1.1751423772589398 chr12 133851895 21700175 0.16212079029587143 1.122438140591253 chr13 115169878 14698029 0.12762042693142386 0.9909420902026375 chr14 107349540 19148362 0.17837395483948976 1.1779582135044961 chr15 102531392 13444568 0.13112635786706184 0.999433909691125 chr16 90354753 12819350 0.14187798178143435 1.47803816203835 chr17 81195210 14222986 0.17517025942786527 1.244426505669151 chr18 78077248 9854411 0.12621360578692528 1.5066876493158883 chr19 59128983 6904055 0.1167626204563674 1.1114473063335988 chr20 63025520 21233424 0.336902004140545 1.6286264744816241 chr21 48129895 6602416 0.13717910666541033 1.0989707658719072 chr22 51304566 5722533 0.11154042312725149 0.8776986956671785 chrMT 16571 1586932 95.76561462796451 70.31762580924489 chrX 155270560 21244820 0.13682452101673362 1.0287933228289352 chrY 59373566 1004030 0.016910387359923774 0.7461078603280977