BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617580.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 49,353,382 number of mapped reads = 47,974,583 (97.21%) number of supplementary alignments = 3,675,650 (7.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,252,873 number of mapped paired reads (second in pair) = 23,721,710 number of mapped paired reads (both in pair) = 47,114,368 number of mapped paired reads (singletons) = 860,215 number of mapped bases = 6,403,138,767 bp number of sequenced bases = 6,398,170,240 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,451,316 duplication rate = 17.26% >>>>>>> Insert size mean insert size = 690,208.615 std insert size = 8,056,426.5093 median insert size = 272 >>>>>>> Mapping quality mean mapping quality = 52.148 >>>>>>> ACTG content number of A's = 1,837,590,243 bp (28.72%) number of C's = 1,252,888,600 bp (19.58%) number of T's = 1,870,954,513 bp (29.24%) number of G's = 1,436,635,186 bp (22.45%) number of N's = 101,698 bp (0%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 84,413,835 number of insertions = 1,126,098 mapped reads with insertion percentage = 2.23% number of deletions = 2,417,555 mapped reads with deletion percentage = 4.84% homopolymer indels = 44.89% >>>>>>> Coverage mean coverageData = 2.0684X std coverageData = 26.9717X There is a 45.64% of reference with a coverageData >= 1X There is a 32.36% of reference with a coverageData >= 2X There is a 23.62% of reference with a coverageData >= 3X There is a 17.85% of reference with a coverageData >= 4X There is a 13.7% of reference with a coverageData >= 5X There is a 10.68% of reference with a coverageData >= 6X There is a 8.43% of reference with a coverageData >= 7X There is a 6.73% of reference with a coverageData >= 8X There is a 5.42% of reference with a coverageData >= 9X There is a 4.4% of reference with a coverageData >= 10X There is a 3.6% of reference with a coverageData >= 11X There is a 2.97% of reference with a coverageData >= 12X There is a 2.46% of reference with a coverageData >= 13X There is a 2.06% of reference with a coverageData >= 14X There is a 1.72% of reference with a coverageData >= 15X There is a 1.45% of reference with a coverageData >= 16X There is a 1.23% of reference with a coverageData >= 17X There is a 1.05% of reference with a coverageData >= 18X There is a 0.9% of reference with a coverageData >= 19X There is a 0.77% of reference with a coverageData >= 20X There is a 0.66% of reference with a coverageData >= 21X There is a 0.57% of reference with a coverageData >= 22X There is a 0.5% of reference with a coverageData >= 23X There is a 0.44% 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 0.29% of reference with a coverageData >= 27X There is a 0.26% of reference with a coverageData >= 28X There is a 0.23% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.15% of reference with a coverageData >= 33X There is a 0.14% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.1% of reference with a coverageData >= 37X There is a 0.09% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 560597038 2.2491299550262704 16.802525048416342 chr2 243199373 607175309 2.496615437409043 26.656384150352704 chr3 198022430 477708603 2.412396429030792 5.483164952867214 chr4 191154276 290714991 1.5208395913675508 15.819498190497008 chr5 180915260 281045192 1.5534631628089306 3.7050965822924025 chr6 171115067 400477146 2.3403967460095143 18.324972277378873 chr7 159138663 339821948 2.1353827008085395 29.71735206246076 chr8 146364022 379735389 2.5944585548489507 8.420226337046298 chr9 141213431 264229410 1.871135118868403 46.40488967775156 chr10 135534747 282320528 2.083012173992548 78.61215640174856 chr11 135006516 272625424 2.019350117886162 20.228278804185326 chr12 133851895 310579389 2.3203211953032117 9.89809947735167 chr13 115169878 126383996 1.0973702342551757 2.625166669841538 chr14 107349540 204676034 1.9066316818870392 4.371319026004187 chr15 102531392 153425972 1.4963804646288232 5.986327999901218 chr16 90354753 142689983 1.579219446264216 12.037453030428434 chr17 81195210 177603299 2.1873617791000233 22.723852433616912 chr18 78077248 228171064 2.922375850132423 37.90524479612099 chr19 59128983 102865300 1.7396764628946857 10.112358817322297 chr20 63025520 152499328 2.419644106070049 6.514612419749036 chr21 48129895 87908926 1.826493201366843 8.78577276767734 chr22 51304566 52974752 1.0325543344426693 3.3347182354484373 chrMT 16571 562568 33.94894695552471 16.845433950941743 chrX 155270560 332358020 2.1405089284150196 7.489709097060134 chrY 59373566 173989158 2.9304144878210616 75.46411989435335