BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084350.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 = 2,098,144 number of mapped reads = 1,895,093 (90.32%) number of supplementary alignments = 12,731 (0.61%) number of secondary alignments = 0 number of mapped bases = 126,559,607 bp number of sequenced bases = 126,517,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,205 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4764 >>>>>>> ACTG content number of A's = 35,034,127 bp (27.69%) number of C's = 24,474,326 bp (19.34%) number of T's = 38,710,799 bp (30.6%) number of G's = 28,143,611 bp (22.24%) number of N's = 154,751 bp (0.12%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,226,487 number of insertions = 8,770 mapped reads with insertion percentage = 0.46% number of deletions = 24,229 mapped reads with deletion percentage = 1.27% homopolymer indels = 46.83% >>>>>>> Coverage mean coverageData = 0.0409X std coverageData = 0.3001X There is a 3.53% of reference with a coverageData >= 1X There is a 0.42% 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 12574137 0.05044776598570641 0.4828867803448248 chr2 243199373 12281445 0.05049949285847871 0.344947747459677 chr3 198022430 8616977 0.04351515633860265 0.23649236479256674 chr4 191154276 6109392 0.0319605301426791 0.21042347188677996 chr5 180915260 6491932 0.035883827599728184 0.2122708767457216 chr6 171115067 6115800 0.03574086202473333 0.23162265550193617 chr7 159138663 7265822 0.04565717634563764 0.425845233350543 chr8 146364022 6341879 0.04332949391073716 0.28151444776709966 chr9 141213431 4571138 0.03237041949642878 0.24531613107710562 chr10 135534747 9025314 0.06659040725549147 0.436686653780303 chr11 135006516 7124088 0.05276847526381616 0.30569421310558487 chr12 133851895 4711064 0.035196094907733656 0.21225792378852287 chr13 115169878 3137964 0.027246395103414107 0.18445009468612716 chr14 107349540 3489612 0.03250700468767728 0.2071691412804122 chr15 102531392 2865245 0.02794505120929208 0.19344717307011927 chr16 90354753 2825277 0.031268714773643395 0.2149765637201887 chr17 81195210 3509851 0.04322731599561107 0.24641473297617003 chr18 78077248 3461252 0.044331121916592144 0.3847557602766323 chr19 59128983 2692233 0.045531528928884166 0.3759908822080278 chr20 63025520 2595559 0.04118266695776568 0.22996309794239028 chr21 48129895 1356418 0.02818244253389707 0.19907110272028167 chr22 51304566 1116145 0.021755276128834225 0.16465734924528794 chrMT 16571 41196 2.4860298111158046 2.1765015261374123 chrX 155270560 7941612 0.05114692701565577 0.27830218429794795 chrY 59373566 298255 0.005023363427421557 0.1129986617889907