BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124778.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 612,528 number of mapped reads = 543,650 (88.76%) number of supplementary alignments = 227,050 (37.07%) number of secondary alignments = 0 number of mapped bases = 81,203,398 bp number of sequenced bases = 81,168,664 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 768,477 duplication rate = 27.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6089 >>>>>>> ACTG content number of A's = 23,308,099 bp (28.72%) number of C's = 15,569,932 bp (19.18%) number of T's = 25,876,524 bp (31.88%) number of G's = 16,414,109 bp (20.22%) number of N's = 0 bp (0%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 657,764 number of insertions = 11,217 mapped reads with insertion percentage = 2.04% number of deletions = 33,174 mapped reads with deletion percentage = 5.94% homopolymer indels = 76.92% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 41.0123X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 46770 1.876424612799661E-4 0.11711128053599122 chr2 243199373 21406 8.801831902749191E-5 0.0283071309678554 chr3 198022430 17132 8.65154518101813E-5 0.05558450740516717 chr4 191154276 8560 4.478058340688126E-5 0.012230239049178322 chr5 180915260 58467 3.231734017351549E-4 0.42804440557956336 chr6 171115067 9946 5.812463025246047E-5 0.009292041142787257 chr7 159138663 12341 7.754872239940837E-5 0.020548377509644083 chr8 146364022 56712393 0.3874749561063579 169.12139597944596 chr9 141213431 6547 4.636244550987505E-5 0.006940178329528769 chr10 135534747 24199596 0.17854901813481083 86.77571435527919 chr11 135006516 8718 6.457466097414142E-5 0.011650958603765804 chr12 133851895 6515 4.867319958376383E-5 0.007128987572192293 chr13 115169878 4384 3.806550876089319E-5 0.00621797197053099 chr14 107349540 5367 4.9995556571551215E-5 0.03607983313976295 chr15 102531392 4856 4.736110478242605E-5 0.021453141754145425 chr16 90354753 55123 6.100730528254556E-4 0.645991932990166 chr17 81195210 3582 4.4115902896242276E-5 0.006716513497652838 chr18 78077248 2921 3.741166696858988E-5 0.006961567796310584 chr19 59128983 2109 3.5667787487567643E-5 0.005972144949388233 chr20 63025520 4604 7.304977412324405E-5 0.008864642102706525 chr21 48129895 1199 2.4911751833242106E-5 0.004991105212061022 chr22 51304566 974 1.8984665029619393E-5 0.004357098187109524 chrMT 16571 300 0.018103916480598635 0.13332728411192565 chrX 155270560 8800 5.667526413249234E-5 0.014791084902326163 chrY 59373566 788 1.3271899484696608E-5 0.00409983546853142