BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716127.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 = 1,229,128 number of mapped reads = 1,124,263 (91.47%) number of supplementary alignments = 22,902 (1.86%) number of secondary alignments = 0 number of mapped bases = 88,012,345 bp number of sequenced bases = 87,972,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,354 duplication rate = 2.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0681 >>>>>>> ACTG content number of A's = 22,139,827 bp (25.17%) number of C's = 16,525,406 bp (18.78%) number of T's = 27,638,264 bp (31.42%) number of G's = 21,664,030 bp (24.63%) number of N's = 5,139 bp (0.01%) GC percentage = 43.41% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 584,408 number of insertions = 7,493 mapped reads with insertion percentage = 0.66% number of deletions = 20,684 mapped reads with deletion percentage = 1.81% homopolymer indels = 43.07% >>>>>>> Coverage mean coverageData = 0.0284X std coverageData = 0.2876X There is a 2.54% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8567564 0.03437329048821106 0.5679801794259395 chr2 243199373 7219059 0.02968370728488679 0.30800695845813064 chr3 198022430 5664108 0.028603365790430914 0.18202505353540688 chr4 191154276 5594696 0.029267961549549644 0.2272455986892622 chr5 180915260 5097663 0.028177075830971916 0.18175849643980796 chr6 171115067 4851113 0.028350004970631837 0.19346575473315353 chr7 159138663 4518462 0.02839323841749255 0.33625262660118344 chr8 146364022 4308217 0.02943494542668416 0.31779082939174386 chr9 141213431 3526043 0.02496960080234861 0.24144279586564488 chr10 135534747 4075333 0.030068547661803655 0.29089298296251526 chr11 135006516 4924729 0.03647771341643984 0.31096279118932124 chr12 133851895 3829075 0.028606804558127474 0.1831413361580098 chr13 115169878 3131935 0.027194046346041976 0.17915257259667647 chr14 107349540 2699549 0.0251472805565818 0.1835847265753622 chr15 102531392 2426703 0.023667902606842595 0.1663579524557913 chr16 90354753 1965155 0.021749326236329813 0.17009452406191042 chr17 81195210 2690396 0.03313491029827991 0.22720845227660952 chr18 78077248 2316262 0.029666286393700763 0.40718144672623635 chr19 59128983 1635841 0.02766563734065915 0.4065712618051078 chr20 63025520 1794714 0.0284759887740712 0.19243261559613978 chr21 48129895 1163452 0.024173167217588984 0.19389854387019667 chr22 51304566 969975 0.018906211973413828 0.14925464850438602 chrMT 16571 27965 1.6875867479331361 1.5577925395522576 chrX 155270560 4752124 0.03060544123754046 0.2147764726157778 chrY 59373566 262212 0.004416308766092978 0.15530424504865425