BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234045.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,113,463 number of mapped reads = 3,852,847 (93.66%) number of supplementary alignments = 30,573 (0.74%) number of secondary alignments = 0 number of mapped bases = 245,405,665 bp number of sequenced bases = 245,310,098 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 595,837 duplication rate = 12.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0451 >>>>>>> ACTG content number of A's = 63,185,045 bp (25.76%) number of C's = 43,646,116 bp (17.79%) number of T's = 81,194,769 bp (33.1%) number of G's = 57,260,328 bp (23.34%) number of N's = 23,840 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,336,503 number of insertions = 16,425 mapped reads with insertion percentage = 0.42% number of deletions = 54,256 mapped reads with deletion percentage = 1.4% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0793X std coverageData = 0.9266X There is a 5.45% of reference with a coverageData >= 1X There is a 1.54% of reference with a coverageData >= 2X There is a 0.48% 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 0.01% 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% 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 25460719 0.1021490694701218 1.658955794256599 chr2 243199373 27294354 0.11223036335706342 1.6269406262353838 chr3 198022430 22973315 0.1160137010741662 0.46368564962760433 chr4 191154276 1875671 0.009812341315346772 0.17898930467191265 chr5 180915260 12162376 0.06722692159854288 0.368938625809206 chr6 171115067 14329585 0.08374239189585801 0.7918850476149119 chr7 159138663 24619817 0.15470669751699498 1.6498487906275938 chr8 146364022 10846512 0.07410640847243184 0.7811319778692777 chr9 141213431 19872940 0.14072981485734173 0.7678526717812233 chr10 135534747 11655266 0.0859946711672395 0.5437109719474835 chr11 135006516 1239082 0.0091779421965085 0.3764726698593184 chr12 133851895 1001449 0.007481769309280231 0.2367394403723568 chr13 115169878 10097829 0.08767769121019647 0.4676843662020043 chr14 107349540 15306772 0.142588147094063 0.5661098941669022 chr15 102531392 616520 0.006012987710144421 0.20350875021583278 chr16 90354753 5930211 0.06563252959144274 0.4507389874685023 chr17 81195210 6413058 0.0789832060290256 0.4482605849029501 chr18 78077248 2905581 0.0372141830613702 1.8176308633328027 chr19 59128983 7090328 0.11991290294981059 0.9257230464711864 chr20 63025520 7449928 0.11820494301356022 0.5043566857973076 chr21 48129895 6693920 0.13908029510556796 0.555126486150987 chr22 51304566 2035977 0.0396841286991883 0.26209313950664326 chrMT 16571 155245 9.36847504676845 6.228021115156659 chrX 155270560 6842006 0.04406505650523834 0.37314321899415126 chrY 59373566 537204 0.009047864836011365 0.2392715533675119