BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617725.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 = 32,383,146 number of mapped reads = 31,102,766 (96.05%) number of supplementary alignments = 2,153,976 (6.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,856,305 number of mapped paired reads (second in pair) = 15,246,461 number of mapped paired reads (both in pair) = 30,268,994 number of mapped paired reads (singletons) = 833,772 number of mapped bases = 4,123,647,847 bp number of sequenced bases = 4,120,026,077 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,855,626 duplication rate = 14.84% >>>>>>> Insert size mean insert size = 566,043.5131 std insert size = 7,237,776.3941 median insert size = 271 >>>>>>> Mapping quality mean mapping quality = 51.6357 >>>>>>> ACTG content number of A's = 1,181,096,556 bp (28.67%) number of C's = 809,438,610 bp (19.65%) number of T's = 1,201,446,106 bp (29.16%) number of G's = 928,028,924 bp (22.52%) number of N's = 15,881 bp (0%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0154 number of mismatches = 60,554,258 number of insertions = 900,568 mapped reads with insertion percentage = 2.64% number of deletions = 1,623,708 mapped reads with deletion percentage = 4.94% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 1.3321X std coverageData = 24.2585X There is a 39% of reference with a coverageData >= 1X There is a 24.56% of reference with a coverageData >= 2X There is a 16% of reference with a coverageData >= 3X There is a 10.99% of reference with a coverageData >= 4X There is a 7.69% of reference with a coverageData >= 5X There is a 5.52% of reference with a coverageData >= 6X There is a 4.04% of reference with a coverageData >= 7X There is a 3.01% of reference with a coverageData >= 8X There is a 2.27% of reference with a coverageData >= 9X There is a 1.74% of reference with a coverageData >= 10X There is a 1.35% of reference with a coverageData >= 11X There is a 1.06% of reference with a coverageData >= 12X There is a 0.84% of reference with a coverageData >= 13X There is a 0.68% of reference with a coverageData >= 14X There is a 0.55% of reference with a coverageData >= 15X There is a 0.45% of reference with a coverageData >= 16X There is a 0.37% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.11% of reference with a coverageData >= 25X There is a 0.09% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.07% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 352389755 1.4137968988249783 21.432072115043066 chr2 243199373 340196000 1.3988358432157635 34.88220446648007 chr3 198022430 223354742 1.1279264778237497 3.8020901237731586 chr4 191154276 240816855 1.2598036519988702 15.821372793195238 chr5 180915260 268995080 1.486856774823749 3.9835768822509334 chr6 171115067 260691949 1.5234891559841426 14.213048399187151 chr7 159138663 182371813 1.14599312047758 18.62333973927788 chr8 146364022 243825872 1.6658866616824728 7.843182088706716 chr9 141213431 196792391 1.3935812592783756 36.24895783131689 chr10 135534747 222500045 1.6416457766361567 75.71065243330109 chr11 135006516 157423061 1.166040467261595 13.579143469528331 chr12 133851895 185412554 1.385206791431679 7.1884615039237385 chr13 115169878 131162175 1.13885833064788 2.673801035962611 chr14 107349540 132977459 1.2387333844187876 4.145556315588068 chr15 102531392 96679835 0.9429291177476651 4.2427898342211705 chr16 90354753 140608047 1.5561776478986113 32.36299712332081 chr17 81195210 88034500 1.0842326782577445 16.87452395114643 chr18 78077248 130060320 1.6657902696570452 34.791472812761164 chr19 59128983 68019580 1.1503593762131847 11.38664386373551 chr20 63025520 73008866 1.1584016442863145 5.365845729687756 chr21 48129895 56264189 1.1690071004725857 8.087896162043362 chr22 51304566 37057780 0.722309589364814 4.072405449622824 chrMT 16571 965801 58.28260213626214 29.047382562890505 chrX 155270560 276464228 1.7805321755779073 7.482677541495348 chrY 59373566 17574950 0.2960063069144272 20.716148023178874