BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006397.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,187,564 number of mapped reads = 3,731,560 (89.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,877,786 number of mapped paired reads (second in pair) = 1,853,774 number of mapped paired reads (both in pair) = 3,452,278 number of mapped paired reads (singletons) = 279,282 number of mapped bases = 144,482,372 bp number of sequenced bases = 144,464,743 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,632 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 72,517.1056 std insert size = 2,593,067.36 median insert size = 130 >>>>>>> Mapping quality mean mapping quality = 48.0063 >>>>>>> ACTG content number of A's = 39,395,230 bp (27.27%) number of C's = 31,888,322 bp (22.07%) number of T's = 40,166,624 bp (27.8%) number of G's = 33,008,125 bp (22.85%) number of N's = 6,442 bp (0%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 433,644 number of insertions = 3,958 mapped reads with insertion percentage = 0.11% number of deletions = 13,137 mapped reads with deletion percentage = 0.35% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.0467X std coverageData = 0.2863X There is a 4.06% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 12211193 0.048991625180344084 0.35798715188600067 chr2 243199373 12084177 0.04968835589884518 0.2883865172217436 chr3 198022430 9647595 0.048719708166393066 0.24442138470426847 chr4 191154276 8818562 0.04613321859459738 0.2639119736389891 chr5 180915260 8417852 0.04652925353007811 0.2396691889009061 chr6 171115067 8105669 0.04736969772509863 0.2542279145443543 chr7 159138663 7704600 0.048414381865203936 0.30337837222225905 chr8 146364022 7058719 0.04822714560276295 0.4580342892285759 chr9 141213431 5976022 0.04231907657565519 0.24817852444575156 chr10 135534747 6923660 0.051084022018353714 0.3173117765823953 chr11 135006516 6686374 0.04952630582660173 0.2698057694305757 chr12 133851895 6537069 0.04883807584494788 0.2508773530375141 chr13 115169878 4355661 0.037819446157614234 0.21848255683491694 chr14 107349540 4439469 0.04135526803375217 0.2616305613061398 chr15 102531392 4331155 0.04224223348103964 0.22912308819524696 chr16 90354753 4525459 0.050085455936114395 0.27992185048319373 chr17 81195210 4251028 0.052355650043888056 0.2626510457008274 chr18 78077248 3705450 0.04745876801395459 0.34858376243121636 chr19 59128983 3347148 0.056607569252459494 0.3255868313856117 chr20 63025520 3343332 0.053047273548873536 0.2663689529550828 chr21 48129895 1875827 0.038974259137693944 0.2524738598495379 chr22 51304566 2042725 0.03981565695341814 0.22883586749185916 chrMT 16571 754 0.045501176754571236 0.3387628235241865 chrX 155270560 7730572 0.049787751135823816 0.25903120761430437 chrY 59373566 362300 0.006102042110793884 0.1658575342432749