BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124879.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 = 3,650,468 number of mapped reads = 3,572,809 (97.87%) number of supplementary alignments = 16,389 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,789,563 number of mapped paired reads (second in pair) = 1,783,246 number of mapped paired reads (both in pair) = 3,558,962 number of mapped paired reads (singletons) = 13,847 number of mapped bases = 311,324,128 bp number of sequenced bases = 311,155,331 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,205 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 39,205.4129 std insert size = 1,893,631.7671 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.939 >>>>>>> ACTG content number of A's = 87,835,182 bp (28.23%) number of C's = 57,812,350 bp (18.58%) number of T's = 93,233,107 bp (29.96%) number of G's = 72,270,153 bp (23.23%) number of N's = 4,539 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,289,622 number of insertions = 41,232 mapped reads with insertion percentage = 1.13% number of deletions = 103,727 mapped reads with deletion percentage = 2.85% homopolymer indels = 48.49% >>>>>>> Coverage mean coverageData = 0.1006X std coverageData = 0.896X There is a 7.26% of reference with a coverageData >= 1X There is a 1.76% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 23645079 0.0948646743792867 0.9386487684521821 chr2 243199373 26070892 0.10719966782151202 1.0898933095540981 chr3 198022430 30129667 0.15215279905412735 0.5035010234516196 chr4 191154276 18353774 0.09601550320537951 0.5771405387478984 chr5 180915260 16311459 0.09016076919105663 0.383048622072917 chr6 171115067 15315526 0.08950425154554041 0.680251816011807 chr7 159138663 20686266 0.12998893926864272 1.6529872765406575 chr8 146364022 19843397 0.13557564713546885 0.6008711630488555 chr9 141213431 12386399 0.08771402912800837 1.0257514312184164 chr10 135534747 14977946 0.11051000818262494 1.8758482727031118 chr11 135006516 13733728 0.1017264085238671 0.702123870632249 chr12 133851895 16795094 0.1254752052632501 0.4542114945015649 chr13 115169878 6743017 0.05854844267526271 0.2998028666013464 chr14 107349540 8974027 0.08359632467917422 0.3978703726182338 chr15 102531392 8406655 0.08199103548696579 0.36649293538601196 chr16 90354753 9802267 0.10848645671135862 1.6059452483538046 chr17 81195210 6981450 0.08598352045644071 0.8443518301947636 chr18 78077248 8059145 0.10322014679615757 1.0664520838907547 chr19 59128983 3714298 0.06281687611640471 0.6263703232255927 chr20 63025520 9215785 0.14622306963909223 0.5085728107711013 chr21 48129895 3716691 0.07722208826759336 0.43858029906191665 chr22 51304566 2903631 0.056595956780922774 0.30784898499302005 chrMT 16571 99641 6.012974473477763 4.070763652057973 chrX 155270560 11721568 0.07549124573261022 0.49311530179788854 chrY 59373566 2736726 0.04609334059537539 0.7690874485873038