BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716454.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 = 32,467,814 number of mapped reads = 31,507,004 (97.04%) number of supplementary alignments = 16,475 (0.05%) number of secondary alignments = 0 number of mapped bases = 2,138,758,777 bp number of sequenced bases = 2,138,378,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,795,101 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1509 >>>>>>> ACTG content number of A's = 619,957,919 bp (28.99%) number of C's = 452,717,692 bp (21.17%) number of T's = 637,795,633 bp (29.83%) number of G's = 427,573,173 bp (20%) number of N's = 334,193 bp (0.02%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 7,368,184 number of insertions = 179,309 mapped reads with insertion percentage = 0.57% number of deletions = 203,168 mapped reads with deletion percentage = 0.64% homopolymer indels = 39.7% >>>>>>> Coverage mean coverageData = 0.6909X std coverageData = 6.3009X There is a 46.13% of reference with a coverageData >= 1X There is a 15.16% of reference with a coverageData >= 2X There is a 3.83% of reference with a coverageData >= 3X There is a 0.87% of reference with a coverageData >= 4X There is a 0.23% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 197359413 0.7918111184966716 14.89982150726993 chr2 243199373 179759513 0.739144639982275 4.165369994435402 chr3 198022430 140226934 0.7081366186648654 2.602842116988258 chr4 191154276 141080439 0.7380449025372574 2.6445455131188402 chr5 180915260 120941603 0.6684986274789645 1.2237878556190858 chr6 171115067 118247872 0.6910430161009725 2.2137719189581135 chr7 159138663 108696329 0.6830290449279444 3.827165944308065 chr8 146364022 117243854 0.801042854643609 4.650784242890597 chr9 141213431 84775614 0.6003367625845731 3.724623148823457 chr10 135534747 110740282 0.8170619302517309 15.148350704466067 chr11 135006516 88606799 0.656314981122837 2.764089707714469 chr12 133851895 94242282 0.7040788029187035 1.3019127313414065 chr13 115169878 64805606 0.562695794468064 0.8548301491465679 chr14 107349540 64026631 0.5964313494030808 1.62932414031108 chr15 102531392 59231762 0.5776939222672408 0.882957417794999 chr16 90354753 68470580 0.7577972129479453 6.002315151876316 chr17 81195210 54059530 0.665797034086124 1.7470820942135732 chr18 78077248 56836794 0.7279559084869385 8.68475356098481 chr19 59128983 41724604 0.705654010656669 10.137693285297178 chr20 63025520 49392957 0.7836977306970256 1.4462641368416511 chr21 48129895 29374252 0.6103119900843332 2.628539409162528 chr22 51304566 25725322 0.5014236354713536 1.0144356849397826 chrMT 16571 4992969 301.3076458873936 66.01357199686703 chrX 155270560 110794891 0.7135601945404203 2.2646190276841436 chrY 59373566 7401945 0.12466734775539674 3.9114618757344997