BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525173.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,676,740 number of mapped reads = 1,575,142 (93.94%) number of supplementary alignments = 5,091 (0.3%) number of secondary alignments = 0 number of mapped bases = 95,677,443 bp number of sequenced bases = 95,646,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,401 duplication rate = 1.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7096 >>>>>>> ACTG content number of A's = 24,802,933 bp (25.93%) number of C's = 19,427,635 bp (20.31%) number of T's = 28,824,804 bp (30.14%) number of G's = 22,588,927 bp (23.62%) number of N's = 2,231 bp (0%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 463,584 number of insertions = 5,413 mapped reads with insertion percentage = 0.34% number of deletions = 19,005 mapped reads with deletion percentage = 1.2% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2843X There is a 2.81% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% 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 10379937 0.041644578289736736 0.5348089919352218 chr2 243199373 7724639 0.03176257777605372 0.3379199559142745 chr3 198022430 9696563 0.04896699328454862 0.2409416270229196 chr4 191154276 4137427 0.02164443865226431 0.16892684759942167 chr5 180915260 4207936 0.023259154589833936 0.16265067260530933 chr6 171115067 5761017 0.033667502815517704 0.2164119735418702 chr7 159138663 5461350 0.03431818451308718 0.40261953588225924 chr8 146364022 5356429 0.03659662345162939 0.25868468330516525 chr9 141213431 3104888 0.02198720035348479 0.20723841923827432 chr10 135534747 5187667 0.038275550106719125 0.32912421215619586 chr11 135006516 4278691 0.03169247771714959 0.2283485504970933 chr12 133851895 3928963 0.02935306220356462 0.18540411683022898 chr13 115169878 2841687 0.02467387349320627 0.16877867556360268 chr14 107349540 3485827 0.032471746036359356 0.19867540522036575 chr15 102531392 2592728 0.025287162784252457 0.17077516487036176 chr16 90354753 2648730 0.029314783252188184 0.20064399683292639 chr17 81195210 1885700 0.02322427640743832 0.17072891404740329 chr18 78077248 1939651 0.024842717304790252 0.4109699195193879 chr19 59128983 1601385 0.027082911268742776 0.3841859315686348 chr20 63025520 1752916 0.027812797101872386 0.18137597515958076 chr21 48129895 1224781 0.025447406440425435 0.1840295939594025 chr22 51304566 842258 0.016416823407101815 0.1373680484283725 chrMT 16571 137392 8.291110977008026 4.932936829239125 chrX 155270560 5205082 0.03352265877060017 0.2106392758656489 chrY 59373566 293799 0.004948313193787282 0.16681618122737307