BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365344.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 548,091,404 number of mapped reads = 525,533,184 (95.88%) number of supplementary alignments = 2,218,482 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 263,320,653 number of mapped paired reads (second in pair) = 262,212,531 number of mapped paired reads (both in pair) = 522,054,680 number of mapped paired reads (singletons) = 3,478,504 number of mapped bases = 53,339,892,922 bp number of sequenced bases = 53,322,472,658 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 386,402,590 duplication rate = 45.31% >>>>>>> Insert size mean insert size = 67,323.1777 std insert size = 2,524,997.1391 median insert size = 186 >>>>>>> Mapping quality mean mapping quality = 53.783 >>>>>>> ACTG content number of A's = 15,855,979,201 bp (29.74%) number of C's = 10,556,104,041 bp (19.8%) number of T's = 15,327,690,101 bp (28.75%) number of G's = 11,556,772,996 bp (21.67%) number of N's = 25,926,319 bp (0.05%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 365,302,595 number of insertions = 15,599,423 mapped reads with insertion percentage = 2.9% number of deletions = 8,445,606 mapped reads with deletion percentage = 1.57% homopolymer indels = 49.72% >>>>>>> Coverage mean coverageData = 17.2304X std coverageData = 113.9044X There is a 80.9% of reference with a coverageData >= 1X There is a 76.59% of reference with a coverageData >= 2X There is a 72.5% of reference with a coverageData >= 3X There is a 69.39% of reference with a coverageData >= 4X There is a 66.18% of reference with a coverageData >= 5X There is a 63.49% of reference with a coverageData >= 6X There is a 60.63% of reference with a coverageData >= 7X There is a 58.13% of reference with a coverageData >= 8X There is a 55.49% of reference with a coverageData >= 9X There is a 53.12% of reference with a coverageData >= 10X There is a 50.63% of reference with a coverageData >= 11X There is a 48.38% of reference with a coverageData >= 12X There is a 46.04% of reference with a coverageData >= 13X There is a 43.9% of reference with a coverageData >= 14X There is a 41.72% of reference with a coverageData >= 15X There is a 39.71% of reference with a coverageData >= 16X There is a 37.68% of reference with a coverageData >= 17X There is a 35.82% of reference with a coverageData >= 18X There is a 33.95% of reference with a coverageData >= 19X There is a 32.24% of reference with a coverageData >= 20X There is a 30.53% of reference with a coverageData >= 21X There is a 28.96% of reference with a coverageData >= 22X There is a 27.41% of reference with a coverageData >= 23X There is a 25.99% of reference with a coverageData >= 24X There is a 24.6% of reference with a coverageData >= 25X There is a 23.31% of reference with a coverageData >= 26X There is a 22.06% of reference with a coverageData >= 27X There is a 20.9% of reference with a coverageData >= 28X There is a 19.77% of reference with a coverageData >= 29X There is a 18.74% of reference with a coverageData >= 30X There is a 17.73% of reference with a coverageData >= 31X There is a 16.8% of reference with a coverageData >= 32X There is a 15.9% of reference with a coverageData >= 33X There is a 15.06% of reference with a coverageData >= 34X There is a 14.26% of reference with a coverageData >= 35X There is a 13.51% of reference with a coverageData >= 36X There is a 12.79% of reference with a coverageData >= 37X There is a 12.13% of reference with a coverageData >= 38X There is a 11.48% of reference with a coverageData >= 39X There is a 10.89% of reference with a coverageData >= 40X There is a 10.31% of reference with a coverageData >= 41X There is a 9.78% of reference with a coverageData >= 42X There is a 9.27% of reference with a coverageData >= 43X There is a 8.8% of reference with a coverageData >= 44X There is a 8.34% of reference with a coverageData >= 45X There is a 7.91% of reference with a coverageData >= 46X There is a 7.5% of reference with a coverageData >= 47X There is a 7.13% of reference with a coverageData >= 48X There is a 6.76% of reference with a coverageData >= 49X There is a 6.42% of reference with a coverageData >= 50X There is a 6.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4413389852 17.706635330709968 297.57892305736334 chr2 243199373 4623996705 19.01319336460625 74.93963893949957 chr3 198022430 3627961682 18.320963347434933 24.44692553093264 chr4 191154276 3637772537 19.03055800331665 87.29079732361589 chr5 180915260 3304381213 18.264800951561522 22.33912657219338 chr6 171115067 3175010548 18.554827483426692 52.8066182959986 chr7 159138663 2951461859 18.54647892197008 87.4914241394396 chr8 146364022 2734844158 18.685221413224077 34.738955443192346 chr9 141213431 2254549548 15.965546138454776 82.95101439156882 chr10 135534747 2655950199 19.59608334975532 192.97499736865475 chr11 135006516 2490399187 18.446511033585963 67.63702787368145 chr12 133851895 2429836561 18.15317266147035 36.356226831494155 chr13 115169878 1767563050 15.34744223658898 19.73824882104998 chr14 107349540 1642478850 15.300287732951627 21.259366400077564 chr15 102531392 1503919857 14.667896608679612 24.562341498462835 chr16 90354753 1538248828 17.024547983657264 43.40817019410578 chr17 81195210 1459234818 17.97193230980005 81.6632945926915 chr18 78077248 1486922375 19.044246731134788 150.19696168208267 chr19 59128983 1038041957 17.55555235915355 143.55097599423908 chr20 63025520 1126291382 17.870402053009638 30.736183032909757 chr21 48129895 756959118 15.727420930380172 59.68522160899191 chr22 51304566 651348898 12.6957296159566 50.961770069066255 chrMT 16571 77896571 4700.776718363406 869.9314526146629 chrX 155270560 1466968196 9.447819316166568 31.329549083100282 chrY 59373566 524464973 8.833307620431624 164.97034515445992