BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524449.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 = 5,324,787 number of mapped reads = 4,941,764 (92.81%) number of supplementary alignments = 11,075 (0.21%) number of secondary alignments = 0 number of mapped bases = 289,683,215 bp number of sequenced bases = 289,594,612 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 470,637 duplication rate = 6.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5121 >>>>>>> ACTG content number of A's = 69,678,621 bp (24.06%) number of C's = 51,774,040 bp (17.88%) number of T's = 94,743,677 bp (32.72%) number of G's = 73,392,508 bp (25.34%) number of N's = 5,766 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 1,320,983 number of insertions = 18,612 mapped reads with insertion percentage = 0.37% number of deletions = 51,300 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.12% >>>>>>> Coverage mean coverageData = 0.0936X std coverageData = 0.7233X There is a 6.83% of reference with a coverageData >= 1X There is a 1.6% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 28271809 0.11342723595460971 1.3668996875876223 chr2 243199373 22486795 0.09246238887301736 0.827121136721953 chr3 198022430 15972311 0.08065910008275325 0.3784529909142758 chr4 191154276 16352428 0.08554570864007248 0.5084530461015621 chr5 180915260 15664939 0.08658716240962758 0.39220121986715817 chr6 171115067 12441236 0.072706841180736 0.5471996193282836 chr7 159138663 14603189 0.09176392917163066 1.0770284503398115 chr8 146364022 26699756 0.1824202125300984 0.735804569017777 chr9 141213431 12159595 0.08610792127839455 0.6186740769253837 chr10 135534747 15185438 0.11204092187518526 0.7513311336417735 chr11 135006516 9955543 0.07374120372086337 0.7110756830445515 chr12 133851895 13305916 0.09940775212782756 0.41835915903104615 chr13 115169878 6339082 0.05504114539393712 0.3197150969349203 chr14 107349540 6929936 0.06455487373304068 0.3547017429016002 chr15 102531392 7555789 0.07369244533420555 0.39611371742224755 chr16 90354753 8902385 0.0985270249147823 0.4683599935284514 chr17 81195210 10030574 0.12353652389100293 0.5128719101410917 chr18 78077248 6750425 0.08645828551744036 1.1995369684579782 chr19 59128983 5915133 0.10003779364850568 0.934203286336068 chr20 63025520 9130017 0.14486222406415686 0.529952206833397 chr21 48129895 4040080 0.08394117626892808 0.44273486198241 chr22 51304566 2332031 0.045454648227606094 0.27748123992814094 chrMT 16571 341282 20.595136081105547 12.871651895965535 chrX 155270560 17387082 0.11197925736855718 0.5482855103536247 chrY 59373566 930444 0.015671014269211993 0.3662433873661479