BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716983.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 = 1,423,235 number of mapped reads = 1,084,644 (76.21%) number of supplementary alignments = 1,309 (0.09%) number of secondary alignments = 0 number of mapped bases = 57,383,306 bp number of sequenced bases = 57,367,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,559 duplication rate = 5.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1011 >>>>>>> ACTG content number of A's = 11,687,097 bp (20.37%) number of C's = 10,126,161 bp (17.65%) number of T's = 19,125,070 bp (33.34%) number of G's = 16,428,050 bp (28.64%) number of N's = 1,010 bp (0%) GC percentage = 46.29% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 404,434 number of insertions = 3,260 mapped reads with insertion percentage = 0.3% number of deletions = 9,373 mapped reads with deletion percentage = 0.86% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0185X std coverageData = 0.1807X There is a 1.61% of reference with a coverageData >= 1X There is a 0.18% 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% 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 5705902 0.02289222781916359 0.22842385794193146 chr2 243199373 5085133 0.020909317887098336 0.2674150201727819 chr3 198022430 3728091 0.018826609692649463 0.1557411488936983 chr4 191154276 3834756 0.02006105267558859 0.16991723179740628 chr5 180915260 3569668 0.019731160323346965 0.15873103875413705 chr6 171115067 2421882 0.014153528631116978 0.15412706526398356 chr7 159138663 3406129 0.02140352907200182 0.19985943670166284 chr8 146364022 3584566 0.024490759074658388 0.18563211099294172 chr9 141213431 2565759 0.018169369456082402 0.16666211334433892 chr10 135534747 2976016 0.021957587009034666 0.20498363534026418 chr11 135006516 2418075 0.0179108021719485 0.17276717942230072 chr12 133851895 2607613 0.019481330466034865 0.15808094570387562 chr13 115169878 960698 0.00834157347982951 0.10433821679885696 chr14 107349540 1817673 0.0169322849450496 0.1490217142356246 chr15 102531392 1126067 0.010982655926489324 0.12021952319562314 chr16 90354753 1468319 0.016250600563315135 0.15709195113847918 chr17 81195210 2196442 0.02705137408967844 0.192462976412659 chr18 78077248 1536954 0.019685043202342378 0.19186086513371978 chr19 59128983 1482678 0.025075317124936852 0.22152865495568952 chr20 63025520 1476147 0.023421417229084345 0.18161149438329185 chr21 48129895 808451 0.016797273295526615 0.15672343990268953 chr22 51304566 615007 0.011987373599457014 0.12477883324137272 chrMT 16571 8733 0.5270050087502263 0.8995357246152303 chrX 155270560 1812152 0.011670931050934575 0.12744534780055325 chrY 59373566 170395 0.0028698798384452773 0.0914767203963818