BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472475.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 = 19,102,790 number of mapped reads = 18,892,013 (98.9%) number of supplementary alignments = 74,678 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,469,695 number of mapped paired reads (second in pair) = 9,422,318 number of mapped paired reads (both in pair) = 18,787,612 number of mapped paired reads (singletons) = 104,401 number of mapped bases = 1,853,791,793 bp number of sequenced bases = 1,853,572,415 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,274,012 duplication rate = 47.49% >>>>>>> Insert size mean insert size = 29,739.1056 std insert size = 1,680,197.2042 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 55.0216 >>>>>>> ACTG content number of A's = 496,171,809 bp (26.77%) number of C's = 433,349,350 bp (23.38%) number of T's = 494,054,078 bp (26.65%) number of G's = 429,705,304 bp (23.18%) number of N's = 291,874 bp (0.02%) GC percentage = 46.56% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 10,341,399 number of insertions = 93,705 mapped reads with insertion percentage = 0.49% number of deletions = 86,337 mapped reads with deletion percentage = 0.45% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.5988X std coverageData = 20.4336X There is a 5.7% of reference with a coverageData >= 1X There is a 2.69% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.79% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.4% 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 0.33% 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 0.28% 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 0.26% 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 0.23% 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 0.18% 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 0.17% 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 192511989 0.7723631268304844 28.537151213578298 chr2 243199373 132516230 0.5448872189320981 18.242157439698413 chr3 198022430 218548243 1.1036539800062044 25.629252768400608 chr4 191154276 87447504 0.4574708232004185 23.41410929045297 chr5 180915260 101747941 0.5624066261740441 19.700313041398086 chr6 171115067 131329206 0.7674906032675661 20.57887788795932 chr7 159138663 78552305 0.49360918031591106 16.148762982879962 chr8 146364022 92113116 0.6293426126264827 21.37735096160933 chr9 141213431 107257062 0.7595386730600717 20.923146820782474 chr10 135534747 53410734 0.39407410411147187 16.37753363026106 chr11 135006516 71109236 0.5267096589619422 15.898571426861407 chr12 133851895 71129674 0.5314058049010064 16.19178856482012 chr13 115169878 39227993 0.34060983376226206 13.170154510084814 chr14 107349540 53348885 0.49696426272529903 24.511837624512946 chr15 102531392 45815049 0.4468392372942718 14.825485777462251 chr16 90354753 64495966 0.7138082265578215 19.977216755502305 chr17 81195210 75247949 0.9267535486391377 20.61349926487686 chr18 78077248 26995898 0.3457588310489632 16.69063513208771 chr19 59128983 44880962 0.7590349050989089 24.172685149699422 chr20 63025520 45872468 0.7278395799035058 24.923682584507322 chr21 48129895 6574008 0.13658887059695435 4.930185703925324 chr22 51304566 21016594 0.40964373424384876 13.978014409955652 chrMT 16571 1131 0.06825176513185686 0.33483123787401775 chrX 155270560 89905970 0.5790277950952196 21.348390687430047 chrY 59373566 2735680 0.0460757233277853 1.7709831486478815