BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549095.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,689,476 number of mapped reads = 6,699,257 (87.12%) number of secondary alignments = 0 number of mapped bases = 266,100,788 bp number of sequenced bases = 266,076,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 231,717 duplication rate = 2.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9438 >>>>>>> ACTG content number of A's = 79,673,997 bp (29.94%) number of C's = 53,634,253 bp (20.16%) number of T's = 80,611,044 bp (30.3%) number of G's = 52,093,063 bp (19.58%) number of N's = 63,886 bp (0.02%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.004 number of mismatches = 1,050,259 number of insertions = 6,094 mapped reads with insertion percentage = 0.09% number of deletions = 19,470 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.16% >>>>>>> Coverage mean coverageData = 0.086X std coverageData = 0.8106X There is a 7.31% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 21489884 0.08621797576183371 1.9279901389603364 chr2 243199373 23549937 0.09683387218272146 0.5220656452320881 chr3 198022430 19254631 0.09723459610105785 0.3578881838147732 chr4 191154276 18964888 0.0992124706642712 0.36414540029970277 chr5 180915260 17394967 0.09614980516292546 0.36103978744639564 chr6 171115067 16507694 0.09647130605979894 0.44175240291978823 chr7 159138663 15019580 0.09438045863185365 0.7866149041373576 chr8 146364022 14353348 0.098066094412191 1.646941274749707 chr9 141213431 11274701 0.07984156266269035 0.50553918054951 chr10 135534747 12614071 0.09306890874264147 0.590037205806866 chr11 135006516 12309225 0.09117504372900045 0.5159672365991788 chr12 133851895 12284163 0.09177429277336716 0.36381172609048723 chr13 115169878 9316587 0.08089430293570338 0.31575957277287153 chr14 107349540 8224668 0.07661577310904173 0.36838957421837437 chr15 102531392 7440257 0.07256564896729384 0.3006920311841887 chr16 90354753 6740539 0.0746008237109563 0.3795761483309986 chr17 81195210 5896678 0.07262347126142046 0.3487371250405785 chr18 78077248 7386756 0.09460830381726569 0.9957078306946902 chr19 59128983 3993770 0.06754335686781557 1.439411645634171 chr20 63025520 5086222 0.08070099223298753 0.3324071243174699 chr21 48129895 3423804 0.07113674359771614 0.3461761962958692 chr22 51304566 2363869 0.04607521677505273 0.2760503802224278 chrMT 16571 19786 1.1940136382837487 1.6732589279337284 chrX 155270560 8976166 0.057809838516715596 0.34995012115891205 chrY 59373566 2214597 0.03729937662831301 0.3393809348478206