BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714124.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 641,516 number of mapped reads = 523,435 (81.59%) number of supplementary alignments = 17,201 (2.68%) number of secondary alignments = 0 number of mapped bases = 67,978,062 bp number of sequenced bases = 66,520,697 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,620 duplication rate = 44.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.5619 >>>>>>> ACTG content number of A's = 17,771,843 bp (26.72%) number of C's = 14,703,742 bp (22.1%) number of T's = 16,795,253 bp (25.25%) number of G's = 17,249,363 bp (25.93%) number of N's = 496 bp (0%) GC percentage = 48.03% >>>>>>> Mismatches and indels general error rate = 0.0436 number of mismatches = 2,695,878 number of insertions = 71,353 mapped reads with insertion percentage = 13.07% number of deletions = 228,916 mapped reads with deletion percentage = 41.41% homopolymer indels = 29.12% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 5.7831X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 5318996 0.021339950844094388 4.091571630690217 chr2 243199373 8209527 0.03375636581102534 10.330800975463912 chr3 198022430 2415999 0.012200633029298752 2.2391001368689927 chr4 191154276 2341901 0.012251366011817595 2.573905604686147 chr5 180915260 3470652 0.01918385436363964 4.402442284361141 chr6 171115067 2610742 0.015257230387549683 2.893912482741183 chr7 159138663 2052650 0.012898499719078324 2.222606514219387 chr8 146364022 2536425 0.01732956614160275 4.080437519962479 chr9 141213431 2563709 0.01815485242335058 3.313663923943268 chr10 135534747 3035652 0.022397592257282925 3.673577113963796 chr11 135006516 3262400 0.02416475957353051 3.9134756897921785 chr12 133851895 3819962 0.028538721846261498 5.809653584703978 chr13 115169878 2327389 0.020208313496693987 6.096339717184716 chr14 107349540 4297133 0.04002935643692558 18.784810366277366 chr15 102531392 2284608 0.02228203436465585 4.101046812422545 chr16 90354753 1345065 0.014886488594573437 1.8378635289818532 chr17 81195210 2252979 0.027747683637988005 4.12715806464722 chr18 78077248 1657167 0.021224710686524196 4.14404691835211 chr19 59128983 2062001 0.034872931942698894 3.9015904390014176 chr20 63025520 2026830 0.032158877864077916 4.284844022154361 chr21 48129895 533808 0.011090986173977732 1.6444347920434441 chr22 51304566 501356 0.00977215166384996 1.1549845864261667 chrMT 16571 120326 7.261239514815038 58.787582633110134 chrX 155270560 6409424 0.04127906797012904 4.7548802082040815 chrY 59373566 521361 0.008781028917818411 2.163073610586387