BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472795.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,827,112 number of mapped reads = 16,699,881 (99.24%) number of supplementary alignments = 55,164 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,372,149 number of mapped paired reads (second in pair) = 8,327,732 number of mapped paired reads (both in pair) = 16,623,010 number of mapped paired reads (singletons) = 76,871 number of mapped bases = 1,641,452,504 bp number of sequenced bases = 1,641,222,070 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,579,687 duplication rate = 46.65% >>>>>>> Insert size mean insert size = 22,769.3186 std insert size = 1,466,283.7471 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 55.2778 >>>>>>> ACTG content number of A's = 441,722,846 bp (26.91%) number of C's = 381,369,919 bp (23.24%) number of T's = 439,049,002 bp (26.75%) number of G's = 378,761,062 bp (23.08%) number of N's = 319,241 bp (0.02%) GC percentage = 46.31% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 9,290,237 number of insertions = 92,030 mapped reads with insertion percentage = 0.55% number of deletions = 87,307 mapped reads with deletion percentage = 0.51% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.5302X std coverageData = 19.3251X There is a 4.69% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.89% of reference with a coverageData >= 3X There is a 0.65% of reference with a coverageData >= 4X There is a 0.48% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 221907212 0.8902975290882024 34.39710253507617 chr2 243199373 101852499 0.41880247363960105 13.745552633146213 chr3 198022430 194939519 0.9844315060672673 23.24622984569972 chr4 191154276 46410718 0.24279194256685108 7.98734932668567 chr5 180915260 66832212 0.36941169031291227 11.806964515079812 chr6 171115067 105823165 0.6184327707390022 17.699309903717523 chr7 159138663 65017127 0.408556448661379 15.579666752007943 chr8 146364022 81632781 0.5577380279970716 18.34839663501526 chr9 141213431 105472753 0.7469031256665664 22.189354575012615 chr10 135534747 36921621 0.27241443111263564 8.48972388624993 chr11 135006516 98511658 0.7296807659268831 29.019704116700833 chr12 133851895 64043626 0.47846633773843844 13.104478756472192 chr13 115169878 26061919 0.22629110538781677 8.145853706215274 chr14 107349540 55742865 0.5192650569345709 24.926467681071284 chr15 102531392 32944121 0.32130765375739756 11.732454386391028 chr16 90354753 52196520 0.5776842752256763 16.47317744309306 chr17 81195210 68996508 0.8497608171713578 22.282517839050126 chr18 78077248 36299761 0.4649211124859319 23.63271737229586 chr19 59128983 31661798 0.5354700249114719 14.797072147138346 chr20 63025520 31510786 0.49996867935401407 25.00216290885944 chr21 48129895 7758476 0.16119868950472466 8.33548362866946 chr22 51304566 24556321 0.47863811965586067 13.108779088542422 chrMT 16571 1143 0.06897592179108081 0.3648750736991548 chrX 155270560 81665418 0.5259555835954993 18.21704793883791 chrY 59373566 2691977 0.04533965502425776 2.0994720991953075