BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472743.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 = 21,252,480 number of mapped reads = 21,086,866 (99.22%) number of supplementary alignments = 75,932 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,575,107 number of mapped paired reads (second in pair) = 10,511,759 number of mapped paired reads (both in pair) = 20,982,158 number of mapped paired reads (singletons) = 104,708 number of mapped bases = 2,079,710,838 bp number of sequenced bases = 2,079,407,412 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,695,904 duplication rate = 47% >>>>>>> Insert size mean insert size = 24,135.9196 std insert size = 1,548,407.8049 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 55.109 >>>>>>> ACTG content number of A's = 574,230,359 bp (27.62%) number of C's = 468,318,529 bp (22.52%) number of T's = 571,765,214 bp (27.5%) number of G's = 464,692,241 bp (22.35%) number of N's = 401,069 bp (0.02%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 12,540,716 number of insertions = 119,109 mapped reads with insertion percentage = 0.56% number of deletions = 117,198 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.29% >>>>>>> Coverage mean coverageData = 0.6718X std coverageData = 21.9326X There is a 6.2% of reference with a coverageData >= 1X There is a 2.68% of reference with a coverageData >= 2X There is a 1.17% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.33% of reference with a coverageData >= 15X There is a 0.32% of reference with a coverageData >= 16X There is a 0.31% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.27% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.26% of reference with a coverageData >= 27X There is a 0.25% of reference with a coverageData >= 28X There is a 0.25% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.24% of reference with a coverageData >= 31X There is a 0.24% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.23% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.22% of reference with a coverageData >= 37X There is a 0.22% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.21% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.19% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 258180368 1.0358263781417019 32.969186220730364 chr2 243199373 133210608 0.5477423989904776 19.042311852614272 chr3 198022430 257357579 1.2996385257973049 27.724248431291574 chr4 191154276 84759383 0.44340824999384265 17.614957705460082 chr5 180915260 101874689 0.5631072193688913 16.9403691731663 chr6 171115067 99307425 0.5803546510606222 14.887699914542127 chr7 159138663 118286023 0.7432890334135834 26.808449308889713 chr8 146364022 97082554 0.6632952051563601 22.5013150338205 chr9 141213431 119667903 0.8474257877071197 22.151465961358078 chr10 135534747 65737090 0.4850201992851324 24.235722481732747 chr11 135006516 122934995 0.9105856416589552 30.063276177414057 chr12 133851895 102963007 0.7692308502617763 21.396026636517906 chr13 115169878 45477438 0.39487267669068815 14.521338277448583 chr14 107349540 42912248 0.39974319405560566 12.7581422154799 chr15 102531392 42537799 0.4148758557769312 11.634376958578828 chr16 90354753 60482381 0.6693879291552045 18.285060735163533 chr17 81195210 85963741 1.058729215676639 27.02270175606398 chr18 78077248 31478937 0.4031768255971317 17.096803044734088 chr19 59128983 32085833 0.5426413811311451 14.226746434439336 chr20 63025520 42095234 0.6679077618082326 17.895591710859698 chr21 48129895 7118643 0.14790481051329948 5.177606831510278 chr22 51304566 29135097 0.5678850689429865 16.16708963637775 chrMT 16571 2381 0.1436847504676845 0.45937400562769454 chrX 155270560 88300673 0.5686890869717994 22.81886582531717 chrY 59373566 10758809 0.1812053700800117 14.289382691570443