BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548945.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 = 4,542,543 number of mapped reads = 4,002,582 (88.11%) number of secondary alignments = 0 number of mapped bases = 158,300,217 bp number of sequenced bases = 158,284,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,359 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.152 >>>>>>> ACTG content number of A's = 44,058,037 bp (27.83%) number of C's = 34,622,675 bp (21.87%) number of T's = 45,047,268 bp (28.46%) number of G's = 34,554,855 bp (21.83%) number of N's = 1,313 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 470,036 number of insertions = 5,101 mapped reads with insertion percentage = 0.13% number of deletions = 12,270 mapped reads with deletion percentage = 0.31% homopolymer indels = 39.7% >>>>>>> Coverage mean coverageData = 0.0511X std coverageData = 0.5403X There is a 4.51% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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% 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 12900104 0.05175555410150814 0.982110258039921 chr2 243199373 13455932 0.055328810407747224 0.4354864997871161 chr3 198022430 10695191 0.05400999775631478 0.25560619115783895 chr4 191154276 10339183 0.05408815966010617 0.2703649220196487 chr5 180915260 9797191 0.0541534804747814 0.26186937835945606 chr6 171115067 9206152 0.05380094319806449 0.2731297329283076 chr7 159138663 9117402 0.05729218675162553 0.7554864842987875 chr8 146364022 8216591 0.056138051467320295 1.2666041102180758 chr9 141213431 6753482 0.047824643535500526 0.43573397201853625 chr10 135534747 7518834 0.05547532397725286 0.40121740765703573 chr11 135006516 7208467 0.053393474726805036 0.3427782932049026 chr12 133851895 7357654 0.0549686203546091 0.2750200542326366 chr13 115169878 5042437 0.04378260260030839 0.2259656447928601 chr14 107349540 4898085 0.045627442837668425 0.28877731319314165 chr15 102531392 4517624 0.04406088625033004 0.23218821625996577 chr16 90354753 4591660 0.0508181346032787 0.28797832824114855 chr17 81195210 4425375 0.05450290725278006 0.26602850171698766 chr18 78077248 4186059 0.05361432564836301 0.8010585235447338 chr19 59128983 3627290 0.06134538116442828 0.9446346347252674 chr20 63025520 3283512 0.05209813421610802 0.26240989271677506 chr21 48129895 2018161 0.041931547949564406 0.2765078174217923 chr22 51304566 1884669 0.03673491751202027 0.2654147750759357 chrMT 16571 8438 0.509202824210971 0.8686379031156161 chrX 155270560 5828881 0.037540155712712055 0.28901157434041236 chrY 59373566 1421843 0.023947407841395277 0.24607300284338934