BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695975.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 399,276,194 number of mapped reads = 391,265,004 (97.99%) number of supplementary alignments = 1,265,025 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 197,307,946 number of mapped paired reads (second in pair) = 193,957,058 number of mapped paired reads (both in pair) = 386,463,750 number of mapped paired reads (singletons) = 4,801,254 number of mapped bases = 38,546,997,824 bp number of sequenced bases = 38,535,748,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,331,631 duplication rate = 10.03% >>>>>>> Insert size mean insert size = 49,763.7954 std insert size = 2,113,551.4872 median insert size = 308 >>>>>>> Mapping quality mean mapping quality = 53.6964 >>>>>>> ACTG content number of A's = 11,274,744,445 bp (29.26%) number of C's = 7,977,120,487 bp (20.7%) number of T's = 11,263,232,645 bp (29.23%) number of G's = 8,013,514,564 bp (20.8%) number of N's = 7,135,961 bp (0.02%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 256,249,043 number of insertions = 3,900,298 mapped reads with insertion percentage = 0.97% number of deletions = 4,617,323 mapped reads with deletion percentage = 1.15% homopolymer indels = 41.91% >>>>>>> Coverage mean coverageData = 12.4518X std coverageData = 137.0637X There is a 92.01% of reference with a coverageData >= 1X There is a 91.71% of reference with a coverageData >= 2X There is a 91.16% of reference with a coverageData >= 3X There is a 90.2% of reference with a coverageData >= 4X There is a 88.69% of reference with a coverageData >= 5X There is a 86.47% of reference with a coverageData >= 6X There is a 83.42% of reference with a coverageData >= 7X There is a 79.41% of reference with a coverageData >= 8X There is a 74.36% of reference with a coverageData >= 9X There is a 68.29% of reference with a coverageData >= 10X There is a 61.35% of reference with a coverageData >= 11X There is a 53.79% of reference with a coverageData >= 12X There is a 45.97% of reference with a coverageData >= 13X There is a 38.25% of reference with a coverageData >= 14X There is a 30.99% of reference with a coverageData >= 15X There is a 24.46% of reference with a coverageData >= 16X There is a 18.82% of reference with a coverageData >= 17X There is a 14.13% of reference with a coverageData >= 18X There is a 10.38% of reference with a coverageData >= 19X There is a 7.49% of reference with a coverageData >= 20X There is a 5.32% of reference with a coverageData >= 21X There is a 3.75% of reference with a coverageData >= 22X There is a 2.63% of reference with a coverageData >= 23X There is a 1.86% of reference with a coverageData >= 24X There is a 1.34% of reference with a coverageData >= 25X There is a 1% of reference with a coverageData >= 26X There is a 0.77% of reference with a coverageData >= 27X There is a 0.62% of reference with a coverageData >= 28X There is a 0.52% of reference with a coverageData >= 29X There is a 0.45% of reference with a coverageData >= 30X There is a 0.4% of reference with a coverageData >= 31X There is a 0.37% of reference with a coverageData >= 32X There is a 0.34% of reference with a coverageData >= 33X There is a 0.32% of reference with a coverageData >= 34X There is a 0.3% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.21% of reference with a coverageData >= 43X There is a 0.2% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3209451126 12.87640172419069 313.19141971979053 chr2 243199373 3359080780 13.812045395363745 87.28113855390545 chr3 198022430 2526058306 12.756425148403643 13.875425063962975 chr4 191154276 2503878257 13.09873003834871 93.78169591966784 chr5 180915260 2296584789 12.694256907902629 12.113330715886192 chr6 171115067 2203140547 12.875199043693797 52.41029929927514 chr7 159138663 2083653470 13.093320194602867 114.21145583325092 chr8 146364022 1917366831 13.099987311089333 78.16202215618263 chr9 141213431 1628055970 11.52904478328269 115.94141400452759 chr10 135534747 2132583572 15.734589241532284 357.13368761099474 chr11 135006516 1781515325 13.195772898842897 61.510381106810044 chr12 133851895 1717963908 12.834811998739353 12.3256315283818 chr13 115169878 1187957125 10.31482489718362 9.429773598240915 chr14 107349540 1171777399 10.915532558406865 11.103844169390673 chr15 102531392 1114459942 10.869451006770687 10.623335883756784 chr16 90354753 1255521354 13.895465510264856 98.34714428594123 chr17 81195210 1127946921 13.891791412325924 57.89891011182789 chr18 78077248 1047783714 13.419834085340712 150.0322862077689 chr19 59128983 816247931 13.80453188244418 167.02251957599952 chr20 63025520 833638834 13.227004457876745 44.91373299562527 chr21 48129895 533912811 11.093163843386735 55.65879888349413 chr22 51304566 512007247 9.979759832682339 52.34251820403346 chrMT 16571 109818333 6627.139762235231 1033.2306539539713 chrX 155270560 1004279131 6.467930115019873 24.04113753304584 chrY 59373566 472314201 7.954957615313185 136.43677613703812