BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080965.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 6,251,386 number of mapped reads = 5,487,842 (87.79%) number of supplementary alignments = 65,778 (1.05%) number of secondary alignments = 0 number of mapped bases = 369,830,606 bp number of sequenced bases = 369,695,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 481,851 duplication rate = 6.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.04 >>>>>>> ACTG content number of A's = 104,578,192 bp (28.29%) number of C's = 65,223,810 bp (17.64%) number of T's = 120,179,609 bp (32.51%) number of G's = 78,985,231 bp (21.36%) number of N's = 729,003 bp (0.2%) GC percentage = 39.01% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 3,696,708 number of insertions = 29,087 mapped reads with insertion percentage = 0.52% number of deletions = 81,853 mapped reads with deletion percentage = 1.48% homopolymer indels = 49.38% >>>>>>> Coverage mean coverageData = 0.1195X std coverageData = 0.7545X There is a 7.41% of reference with a coverageData >= 1X There is a 2.63% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 30212331 0.12121266089042161 1.0223625462998043 chr2 243199373 24976910 0.10270137497435078 0.7257250860509421 chr3 198022430 32773723 0.16550510464900364 0.6030003898671447 chr4 191154276 23133059 0.12101774275768751 0.533922515604727 chr5 180915260 21871258 0.12089227851757779 0.5094423569785839 chr6 171115067 32064784 0.18738726263070685 0.8860016021089452 chr7 159138663 17426521 0.10950526208706429 0.6992444958447948 chr8 146364022 29778084 0.20345221177373768 1.4997423547002169 chr9 141213431 19521182 0.13823884783310733 0.917790018588427 chr10 135534747 15721679 0.11599740544762296 0.620598344426925 chr11 135006516 16643422 0.12327865715755527 0.628335532910578 chr12 133851895 18872025 0.14099184027241451 0.5725666780955508 chr13 115169878 9451666 0.08206717037592069 0.41890754395877394 chr14 107349540 10726413 0.09992043747928496 0.5832395867508132 chr15 102531392 8758225 0.08541993655952705 0.4281198492338039 chr16 90354753 8001978 0.08856178268784598 0.5282698222592592 chr17 81195210 7317884 0.09012704074538387 0.45937484574051773 chr18 78077248 9365365 0.11994998850369316 1.3993388285985822 chr19 59128983 6008853 0.10162280315222062 0.8548457871063928 chr20 63025520 6194680 0.09828843934964757 0.48604290950128076 chr21 48129895 7126896 0.1480762839810891 0.6640423026328279 chr22 51304566 3086512 0.06016057128326551 0.3539130977274421 chrMT 16571 29072 1.7543901997465452 1.8442608742820452 chrX 155270560 10014610 0.06449780306067035 0.4098187209128768 chrY 59373566 753474 0.012690394914127273 0.2472897973441746