BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818945.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,182,538 number of mapped reads = 3,134,948 (98.5%) number of supplementary alignments = 42,250 (1.33%) number of secondary alignments = 0 number of mapped bases = 290,332,116 bp number of sequenced bases = 290,166,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,565,614 duplication rate = 41.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2466 >>>>>>> ACTG content number of A's = 84,584,883 bp (29.15%) number of C's = 62,637,383 bp (21.59%) number of T's = 82,101,879 bp (28.29%) number of G's = 60,829,405 bp (20.96%) number of N's = 13,404 bp (0%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,885,419 number of insertions = 37,420 mapped reads with insertion percentage = 1.16% number of deletions = 89,542 mapped reads with deletion percentage = 2.79% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.0938X std coverageData = 0.9719X There is a 3.8% of reference with a coverageData >= 1X There is a 2.03% of reference with a coverageData >= 2X There is a 1.23% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.3% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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 33933111 0.13614052740915739 1.6416635773964563 chr2 243199373 25752221 0.10588933960779578 1.457188763633992 chr3 198022430 18670385 0.09428419295733316 0.6141327791620084 chr4 191154276 18698070 0.09781664523162432 0.7082275252161173 chr5 180915260 14793515 0.0817704100803879 0.6020680697928525 chr6 171115067 15218453 0.08893695492051557 0.6540096730816718 chr7 159138663 14802016 0.09301332385832599 0.827536201658415 chr8 146364022 18471583 0.1262030295942537 0.8330675267547311 chr9 141213431 10825644 0.07666157477612735 1.1525843706448038 chr10 135534747 14248333 0.10512679084426962 1.2098442774081573 chr11 135006516 11027042 0.08167785027501932 0.7061172007783921 chr12 133851895 12712771 0.09497639910140981 0.6404984565986486 chr13 115169878 4776815 0.04147625301817199 0.4016515836838926 chr14 107349540 9025563 0.0840764012589155 0.6543548470560445 chr15 102531392 8446754 0.08238212546651079 0.5827429673459957 chr16 90354753 8789082 0.09727304550320667 1.0734511944101044 chr17 81195210 6283429 0.0773866955944815 0.6344184494911637 chr18 78077248 7377867 0.09449445502997236 1.316270401454663 chr19 59128983 4442329 0.0751294673882688 1.4246894309262288 chr20 63025520 6471542 0.10268129481517962 0.700395891563053 chr21 48129895 3942242 0.08190838563017849 0.6693332067343555 chr22 51304566 3639962 0.07094811015456207 0.6007802970847443 chrMT 16571 25243 1.5233238790658379 2.361201341896806 chrX 155270560 17066448 0.10991425547766427 0.7858152260633616 chrY 59373566 891696 0.015018400612824907 0.8985665029826351