BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085122.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 = 2,009,173 number of mapped reads = 1,825,486 (90.86%) number of supplementary alignments = 17,601 (0.88%) number of secondary alignments = 0 number of mapped bases = 124,340,062 bp number of sequenced bases = 124,292,861 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,097 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.537 >>>>>>> ACTG content number of A's = 35,358,936 bp (28.45%) number of C's = 23,067,616 bp (18.56%) number of T's = 39,014,665 bp (31.39%) number of G's = 26,831,333 bp (21.59%) number of N's = 20,311 bp (0.02%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,092,550 number of insertions = 10,083 mapped reads with insertion percentage = 0.55% number of deletions = 28,909 mapped reads with deletion percentage = 1.57% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.0402X std coverageData = 0.3687X There is a 3.6% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9425061 0.037813590843571054 0.6413057168337656 chr2 243199373 10599938 0.04358538375014643 0.42329346894218645 chr3 198022430 8618245 0.043521559653621054 0.22476467037356773 chr4 191154276 8341666 0.043638396035671205 0.23385173963097913 chr5 180915260 7920101 0.04377795991338707 0.2271472368414782 chr6 171115067 7411651 0.04331384214108977 0.27893204644491937 chr7 159138663 7014840 0.044080048605158885 0.4813513513129589 chr8 146364022 6461005 0.04414339611410788 0.6545227569146326 chr9 141213431 5267180 0.03729942656800117 0.33755152325158383 chr10 135534747 5568909 0.04108842288243619 0.32072618853996054 chr11 135006516 5393861 0.039952597547217646 0.28128230325169257 chr12 133851895 5692784 0.04253046996458287 0.22693362040207116 chr13 115169878 4121416 0.03578553760385159 0.2052252849339273 chr14 107349540 3831910 0.03569563502554366 0.2195400320190785 chr15 102531392 3546985 0.034594136788857796 0.2034416974228783 chr16 90354753 3346833 0.037041028710465294 0.2335804033300174 chr17 81195210 3067106 0.03777446970086043 0.22577202951287573 chr18 78077248 3457929 0.04428856150257755 0.6043596281213673 chr19 59128983 2275167 0.03847803369119337 0.489317445268215 chr20 63025520 2416957 0.038348862492526836 0.22006822910645393 chr21 48129895 1648483 0.034250708421449914 0.21277624262313277 chr22 51304566 1274127 0.02483457320348446 0.16877925857812445 chrMT 16571 700 0.042242471788063486 0.20114185383777825 chrX 155270560 7331078 0.04721486159385269 0.2651250167245247 chrY 59373566 306130 0.00515599820970834 0.11394863454178922