BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716550.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 = 1,742,521 number of mapped reads = 1,534,468 (88.06%) number of supplementary alignments = 5,583 (0.32%) number of secondary alignments = 0 number of mapped bases = 86,905,995 bp number of sequenced bases = 86,879,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,796 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1205 >>>>>>> ACTG content number of A's = 20,616,513 bp (23.73%) number of C's = 16,900,914 bp (19.45%) number of T's = 27,335,809 bp (31.46%) number of G's = 22,025,750 bp (25.35%) number of N's = 699 bp (0%) GC percentage = 44.81% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 470,891 number of insertions = 5,248 mapped reads with insertion percentage = 0.34% number of deletions = 16,328 mapped reads with deletion percentage = 1.06% homopolymer indels = 40.82% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.2412X There is a 2.55% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 7378694 0.029603513003885355 0.31822017599010627 chr2 243199373 6814909 0.02802190201370297 0.3559888986072573 chr3 198022430 5025447 0.02537817054360963 0.1739055408850025 chr4 191154276 5302807 0.027740980275010953 0.192472089705497 chr5 180915260 4939626 0.02730353426239445 0.17716806267828353 chr6 171115067 4679305 0.02734595545581033 0.2119026361481591 chr7 159138663 4994375 0.03138379389300261 0.33598831215045916 chr8 146364022 4489034 0.03067033782386767 0.2292627321669542 chr9 141213431 2898921 0.02052864928974072 0.18006247741053125 chr10 135534747 3874879 0.028589561612565668 0.3017894904281431 chr11 135006516 3110930 0.023042813726116745 0.2020232290331104 chr12 133851895 4382034 0.032737930232515575 0.19716745654845763 chr13 115169878 2628554 0.022823276759918076 0.16321335239137996 chr14 107349540 2919102 0.027192496586385 0.18355738212968048 chr15 102531392 3225287 0.03145658063434855 0.1952340322612393 chr16 90354753 3041984 0.033667116548921336 0.21392128871437927 chr17 81195210 3920244 0.04828171514058526 0.2503765077494903 chr18 78077248 1621396 0.020766561854229287 0.27500300859477855 chr19 59128983 2253802 0.03811670496683496 0.3035197769491022 chr20 63025520 2501562 0.03969125522486764 0.2249374229082741 chr21 48129895 1083605 0.022514177518982745 0.17564861274491445 chr22 51304566 810354 0.015794968424447834 0.13712851835087192 chrMT 16571 30983 1.8697121477279586 1.7612612881672298 chrX 155270560 4715021 0.030366484155141836 0.20143818247655426 chrY 59373566 263140 0.004431938617262773 0.12331483432017944