BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085010.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,204,722 number of mapped reads = 1,852,133 (84.01%) number of supplementary alignments = 40,133 (1.82%) number of secondary alignments = 0 number of mapped bases = 121,787,808 bp number of sequenced bases = 121,753,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,028 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7277 >>>>>>> ACTG content number of A's = 37,190,885 bp (30.55%) number of C's = 22,637,078 bp (18.59%) number of T's = 36,287,100 bp (29.8%) number of G's = 25,622,589 bp (21.04%) number of N's = 15,677 bp (0.01%) GC percentage = 39.64% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,070,511 number of insertions = 10,188 mapped reads with insertion percentage = 0.55% number of deletions = 21,667 mapped reads with deletion percentage = 1.16% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.4599X There is a 3.61% of reference with a coverageData >= 1X There is a 0.19% 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 0.01% 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 9352664 0.03752313218910696 0.9080227221825786 chr2 243199373 10779757 0.044324772991910635 0.46342011873799227 chr3 198022430 8637369 0.04361813457192703 0.2209158042661067 chr4 191154276 8704244 0.04553517808829974 0.2297443214290388 chr5 180915260 7929482 0.04382981291904287 0.22534698953391574 chr6 171115067 7484182 0.04373771480918159 0.3680507067990511 chr7 159138663 6750699 0.04242023197090703 0.43084340240464425 chr8 146364022 6669724 0.0455694227916202 0.828056509376712 chr9 141213431 4998384 0.035395953236204564 0.4140661897398843 chr10 135534747 5548707 0.040939368854246656 0.4193378584367945 chr11 135006516 5558314 0.04117070912340261 0.4716680239907884 chr12 133851895 5466873 0.040842701554580155 0.22670461619591362 chr13 115169878 4214876 0.036597034512791615 0.19940057800471778 chr14 107349540 3679868 0.034279308509379734 0.24725278379126905 chr15 102531392 3101219 0.030246531715867078 0.18644398629173317 chr16 90354753 2896964 0.03206210967119793 0.2652430650129819 chr17 81195210 2442712 0.030084434783776037 0.2596943036775392 chr18 78077248 3506163 0.044906334301127004 0.8508757101259143 chr19 59128983 1508034 0.02550414235942465 0.6417824382466238 chr20 63025520 2150339 0.03411854436107786 0.206959238169014 chr21 48129895 1568051 0.03257956411498508 0.2176709773693554 chr22 51304566 843069 0.01643263096699814 0.13273153546540248 chrMT 16571 36717 2.215738338060467 1.9330820967006472 chrX 155270560 7707441 0.04963877891597737 0.3207068995431544 chrY 59373566 251956 0.004243571962647485 0.09330124437115055