BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777249.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 18,889,854 number of mapped reads = 18,764,951 (99.34%) number of supplementary alignments = 619,620 (3.28%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,384,025 number of mapped paired reads (second in pair) = 9,380,926 number of mapped paired reads (both in pair) = 18,720,868 number of mapped paired reads (singletons) = 44,083 number of mapped bases = 1,706,015,864 bp number of sequenced bases = 1,705,378,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,300,802 duplication rate = 35.4% >>>>>>> Insert size mean insert size = 406,131.5369 std insert size = 6,331,736.7087 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.8546 >>>>>>> ACTG content number of A's = 440,896,472 bp (25.85%) number of C's = 356,109,567 bp (20.88%) number of T's = 497,440,502 bp (29.17%) number of G's = 410,868,377 bp (24.09%) number of N's = 63,847 bp (0%) GC percentage = 44.97% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 7,482,818 number of insertions = 102,144 mapped reads with insertion percentage = 0.53% number of deletions = 360,936 mapped reads with deletion percentage = 1.89% homopolymer indels = 49.4% >>>>>>> Coverage mean coverageData = 0.5511X std coverageData = 8.485X There is a 7.67% of reference with a coverageData >= 1X There is a 3.79% of reference with a coverageData >= 2X There is a 2.18% of reference with a coverageData >= 3X There is a 1.6% of reference with a coverageData >= 4X There is a 1.26% of reference with a coverageData >= 5X There is a 1.08% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.88% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.76% of reference with a coverageData >= 10X There is a 0.72% of reference with a coverageData >= 11X There is a 0.69% of reference with a coverageData >= 12X There is a 0.66% of reference with a coverageData >= 13X There is a 0.63% of reference with a coverageData >= 14X There is a 0.6% of reference with a coverageData >= 15X There is a 0.58% of reference with a coverageData >= 16X There is a 0.56% of reference with a coverageData >= 17X There is a 0.54% of reference with a coverageData >= 18X There is a 0.52% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.49% of reference with a coverageData >= 21X There is a 0.47% of reference with a coverageData >= 22X There is a 0.46% of reference with a coverageData >= 23X There is a 0.45% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.4% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.38% of reference with a coverageData >= 30X There is a 0.37% of reference with a coverageData >= 31X There is a 0.36% of reference with a coverageData >= 32X There is a 0.35% of reference with a coverageData >= 33X There is a 0.34% of reference with a coverageData >= 34X There is a 0.33% of reference with a coverageData >= 35X There is a 0.33% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.31% of reference with a coverageData >= 38X There is a 0.3% of reference with a coverageData >= 39X There is a 0.3% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.28% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.27% of reference with a coverageData >= 45X There is a 0.26% of reference with a coverageData >= 46X There is a 0.26% of reference with a coverageData >= 47X There is a 0.25% of reference with a coverageData >= 48X There is a 0.25% of reference with a coverageData >= 49X There is a 0.24% of reference with a coverageData >= 50X There is a 0.24% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 169619498 0.6805178551591251 10.730994673434505 chr2 243199373 149160280 0.613325100965618 8.479690999546712 chr3 198022430 102870895 0.5194911253235303 8.017502696778454 chr4 191154276 80983634 0.4236558851552973 6.7879971912903185 chr5 180915260 90304950 0.4991560689794769 7.850617931125048 chr6 171115067 80159625 0.4684545107883457 7.627247168558898 chr7 159138663 111129500 0.6983186731938297 11.768681481957874 chr8 146364022 57291018 0.39142828419951453 6.359343659561092 chr9 141213431 58531800 0.4144917348548808 6.472111928774326 chr10 135534747 70556782 0.5205807629537244 7.840788170532693 chr11 135006516 113626515 0.8416372658635232 10.920658911855199 chr12 133851895 93238099 0.6965766080487691 9.374343899694193 chr13 115169878 51158531 0.44420061815121487 7.193364513191617 chr14 107349540 36924834 0.3439682554764557 6.163720340162957 chr15 102531392 77839710 0.7591792960345257 10.146551861082628 chr16 90354753 53706338 0.5943941654071037 8.200478620438117 chr17 81195210 71811333 0.8844281947173978 10.240471212714787 chr18 78077248 26936761 0.3450014144965765 6.265279515594426 chr19 59128983 85151697 1.440100821622452 14.257856501184198 chr20 63025520 47233290 0.7494311827970638 9.751391701782453 chr21 48129895 11074039 0.23008649821488286 4.044744388054818 chr22 51304566 19262721 0.3754582194497075 5.772704272661708 chrMT 16571 469310 28.32116347836582 18.56691869142709 chrX 155270560 46195827 0.29751826102771833 5.696033374291389 chrY 59373566 778877 0.013118245247388374 0.5259267727063938