BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173942.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 = 14,836,836 number of mapped reads = 14,497,856 (97.72%) number of supplementary alignments = 2,018,201 (13.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,245,421 number of mapped paired reads (second in pair) = 7,252,435 number of mapped paired reads (both in pair) = 14,285,256 number of mapped paired reads (singletons) = 212,600 number of mapped bases = 1,653,107,493 bp number of sequenced bases = 1,651,940,196 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,649,195 duplication rate = 65.36% >>>>>>> Insert size mean insert size = 958,679.2262 std insert size = 9,211,524.5278 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 52.4021 >>>>>>> ACTG content number of A's = 495,916,650 bp (30.02%) number of C's = 324,887,377 bp (19.67%) number of T's = 492,084,479 bp (29.79%) number of G's = 339,040,071 bp (20.52%) number of N's = 11,619 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 14,924,425 number of insertions = 192,530 mapped reads with insertion percentage = 1.27% number of deletions = 494,482 mapped reads with deletion percentage = 3.32% homopolymer indels = 41.07% >>>>>>> Coverage mean coverageData = 0.534X std coverageData = 9.6455X There is a 11.17% of reference with a coverageData >= 1X There is a 8.53% of reference with a coverageData >= 2X There is a 6.45% of reference with a coverageData >= 3X There is a 5.18% of reference with a coverageData >= 4X There is a 3.9% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.4% of reference with a coverageData >= 7X There is a 2.05% of reference with a coverageData >= 8X There is a 1.54% of reference with a coverageData >= 9X There is a 1.36% of reference with a coverageData >= 10X There is a 1.02% of reference with a coverageData >= 11X There is a 0.92% of reference with a coverageData >= 12X There is a 0.69% of reference with a coverageData >= 13X There is a 0.63% of reference with a coverageData >= 14X There is a 0.47% of reference with a coverageData >= 15X There is a 0.43% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.29% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.2% of reference with a coverageData >= 20X There is a 0.15% of reference with a coverageData >= 21X There is a 0.14% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.08% of reference with a coverageData >= 25X There is a 0.07% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 134159566 0.5382516820289086 4.8461866404880825 chr2 243199373 149822591 0.6160484262432699 31.76919715359288 chr3 198022430 111679156 0.5639722530422437 2.2214929752833936 chr4 191154276 112760735 0.5898938666692447 4.517563733255494 chr5 180915260 102730710 0.5678388323903688 2.2481535452061854 chr6 171115067 98356993 0.5748003067432981 3.348259657661932 chr7 159138663 90492114 0.5686368874419914 4.52887249766141 chr8 146364022 84570038 0.5778061906497759 5.356484185369279 chr9 141213431 70938470 0.502349312651429 4.470231057969338 chr10 135534747 81816954 0.6036603587713194 6.6030331612718465 chr11 135006516 73158977 0.5418921928183081 2.4338157633707453 chr12 133851895 74920237 0.5597248884672122 2.487335381373427 chr13 115169878 54866049 0.4763923514792644 2.051197034150208 chr14 107349540 51933816 0.48378238043684213 2.1668578715894244 chr15 102531392 47515719 0.4634260597963987 2.1941693866441043 chr16 90354753 51333493 0.5681327356403708 4.067305900749705 chr17 81195210 44474964 0.5477535435895787 3.0012744572864296 chr18 78077248 46151609 0.5911018918084818 6.370402227820785 chr19 59128983 31064995 0.5253767851884075 3.8022376518636034 chr20 63025520 34630899 0.5494742288520587 2.6472132346920203 chr21 48129895 23799109 0.49447664492099974 3.4933603932828974 chr22 51304566 19905533 0.38798755260886525 2.72490902587598 chrMT 16571 2780721 167.8064691328224 134.50245870089392 chrX 155270560 45925589 0.2957778280699187 1.7001481519468271 chrY 59373566 13318456 0.2243162554864904 3.645615970872365