BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472555.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 = 13,163,144 number of mapped reads = 12,947,727 (98.36%) number of supplementary alignments = 58,396 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,494,989 number of mapped paired reads (second in pair) = 6,452,738 number of mapped paired reads (both in pair) = 12,849,398 number of mapped paired reads (singletons) = 98,329 number of mapped bases = 1,270,072,933 bp number of sequenced bases = 1,269,917,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,005,665 duplication rate = 45% >>>>>>> Insert size mean insert size = 32,934.1284 std insert size = 1,759,234.5255 median insert size = 243 >>>>>>> Mapping quality mean mapping quality = 54.8836 >>>>>>> ACTG content number of A's = 351,223,052 bp (27.66%) number of C's = 285,664,461 bp (22.49%) number of T's = 348,636,953 bp (27.45%) number of G's = 284,196,922 bp (22.38%) number of N's = 195,922 bp (0.02%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 7,992,872 number of insertions = 71,902 mapped reads with insertion percentage = 0.55% number of deletions = 65,449 mapped reads with deletion percentage = 0.5% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.4103X std coverageData = 18.6128X There is a 3.88% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.17% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.15% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.15% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.14% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.13% of reference with a coverageData >= 47X There is a 0.13% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 182593394 0.7325694646915243 44.79378802237906 chr2 243199373 71870601 0.295521325213285 10.639025845916986 chr3 198022430 158509372 0.8004617052724785 21.497855475727103 chr4 191154276 43773411 0.22899519652911138 10.577520101699388 chr5 180915260 69320055 0.38316311736223907 16.071487991114324 chr6 171115067 85844483 0.5016769388285369 16.767712777759208 chr7 159138663 49874018 0.3133997550299892 14.07912154784464 chr8 146364022 42935394 0.29334663951773615 9.865384431386314 chr9 141213431 63943891 0.45281734568151666 12.917256176221738 chr10 135534747 33522252 0.24733326871521735 10.03413169085004 chr11 135006516 35654217 0.26409256424334365 10.064259089303896 chr12 133851895 61814156 0.4618100924159497 14.979136045665772 chr13 115169878 24285848 0.2108697901025822 7.9140056151003035 chr14 107349540 25152599 0.2343056057808911 9.524701276293975 chr15 102531392 42358259 0.41312478231057276 20.944053250371283 chr16 90354753 37902988 0.4194908042081638 11.493031064182608 chr17 81195210 57709962 0.7107557453204444 17.891304071155027 chr18 78077248 20016146 0.25636336465137705 10.834612125394441 chr19 59128983 21099171 0.3568329764778806 10.430962877485046 chr20 63025520 38654623 0.613317002382527 18.768009178591218 chr21 48129895 5703145 0.1184948564712223 4.335482503679257 chr22 51304566 10824914 0.21099318918320056 9.709677602239044 chrMT 16571 2109 0.12727053285860843 0.4360349905184694 chrX 155270560 85057244 0.5478002011456647 20.74478826913347 chrY 59373566 1650681 0.027801614610784873 0.7484394740029247