BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237280.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,071,589 number of mapped reads = 473,264 (22.85%) number of supplementary alignments = 4,259 (0.21%) number of secondary alignments = 0 number of mapped bases = 32,923,583 bp number of sequenced bases = 32,910,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,872 duplication rate = 5.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2853 >>>>>>> ACTG content number of A's = 9,649,377 bp (29.32%) number of C's = 6,190,648 bp (18.81%) number of T's = 10,249,795 bp (31.14%) number of G's = 6,819,777 bp (20.72%) number of N's = 523 bp (0%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 245,688 number of insertions = 2,448 mapped reads with insertion percentage = 0.51% number of deletions = 7,806 mapped reads with deletion percentage = 1.63% homopolymer indels = 49.31% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.2018X There is a 0.54% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2800449 0.011235474514625182 0.25897918199603037 chr2 243199373 2335484 0.009603166205531295 0.18877674614030282 chr3 198022430 1940247 0.009798117314286063 0.17570129102629847 chr4 191154276 2968845 0.015531146161752616 0.22358191251880907 chr5 180915260 3284273 0.018153653815604055 0.23815364059120767 chr6 171115067 1689472 0.009873309402964497 0.17643320295423962 chr7 159138663 1648129 0.010356559298226604 0.18579092229034777 chr8 146364022 1495762 0.010219464999397188 0.1960122424851342 chr9 141213431 1153905 0.008171354465567797 0.16770555658703867 chr10 135534747 1339561 0.009883524554777087 0.18735051317583618 chr11 135006516 1391298 0.01030541370314304 0.22056330983678868 chr12 133851895 922067 0.006888710839693379 0.144585007375434 chr13 115169878 1374169 0.011931670188970766 0.19346241909918466 chr14 107349540 881756 0.008213877767897282 0.15872977125099982 chr15 102531392 1100644 0.01073470259722993 0.1836003399612455 chr16 90354753 612528 0.0067791453095998174 0.13901491637770103 chr17 81195210 1341328 0.016519792238975674 0.24056051100161666 chr18 78077248 1098290 0.014066709933218957 0.2706122535317941 chr19 59128983 813972 0.013766040927847516 0.2387647117107399 chr20 63025520 560961 0.008900537433090596 0.16211874825615083 chr21 48129895 362151 0.007524450240333996 0.15270814949434736 chr22 51304566 286706 0.005588313523595541 0.1264981939463773 chrMT 16571 283341 17.098605998430994 10.444833876064735 chrX 155270560 1170786 0.007540296112798202 0.15737425427330426 chrY 59373566 67459 0.0011361790194646553 0.04946738868574996