BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717064.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 = 1,008,745 number of mapped reads = 823,789 (81.66%) number of supplementary alignments = 2,974 (0.29%) number of secondary alignments = 0 number of mapped bases = 45,012,540 bp number of sequenced bases = 45,000,135 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,741 duplication rate = 1.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4952 >>>>>>> ACTG content number of A's = 10,011,507 bp (22.25%) number of C's = 9,376,993 bp (20.84%) number of T's = 14,111,570 bp (31.36%) number of G's = 11,498,729 bp (25.55%) number of N's = 1,336 bp (0%) GC percentage = 46.39% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 238,272 number of insertions = 3,704 mapped reads with insertion percentage = 0.45% number of deletions = 7,502 mapped reads with deletion percentage = 0.9% homopolymer indels = 33.43% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 0.143X There is a 1.35% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3489214 0.013998817679976813 0.14765195836578773 chr2 243199373 3698087 0.015205989038466806 0.17740153022913463 chr3 198022430 2920070 0.014746157796366805 0.1325484388402609 chr4 191154276 2776185 0.014523269152503814 0.14177264998285755 chr5 180915260 2541340 0.014047129026042358 0.1263106706232533 chr6 171115067 2608520 0.015244244973471564 0.133569800913074 chr7 159138663 2485146 0.015616230230613412 0.157029814787337 chr8 146364022 2225174 0.015203012117281117 0.13779235119716368 chr9 141213431 1882963 0.01333416366039573 0.13162850219566233 chr10 135534747 2222581 0.016398606624469517 0.17265928908562386 chr11 135006516 1992753 0.014760420897018038 0.14781698754653178 chr12 133851895 2114755 0.015799215991674977 0.13412310456417698 chr13 115169878 1322750 0.011485207963839296 0.11516581353575397 chr14 107349540 1366921 0.012733366160674746 0.12437755236192259 chr15 102531392 1332723 0.012998194738251482 0.12288059290725403 chr16 90354753 1505233 0.016659145756283567 0.14616496832796239 chr17 81195210 1414202 0.017417308237764273 0.1442162662086318 chr18 78077248 1132073 0.014499396802510252 0.15998653352935308 chr19 59128983 1162162 0.019654692860183304 0.17321627002903142 chr20 63025520 1056217 0.01675856065923772 0.14179058301158057 chr21 48129895 594281 0.01234744019283649 0.13120918510681262 chr22 51304566 639925 0.012473061364557688 0.1226954304711287 chrMT 16571 12951 0.7815460744674432 1.1165067030724363 chrX 155270560 2347107 0.015116239678661558 0.13756416007230296 chrY 59373566 169207 0.0028498709341460136 0.08736884598035628