BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163026.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 85,335,396 number of mapped reads = 83,687,695 (98.07%) number of supplementary alignments = 459,712 (0.54%) number of secondary alignments = 0 number of mapped bases = 8,168,762,994 bp number of sequenced bases = 8,167,721,802 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,631,887 duplication rate = 45.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9377 >>>>>>> ACTG content number of A's = 1,943,365,629 bp (23.79%) number of C's = 2,141,802,933 bp (26.22%) number of T's = 1,942,505,421 bp (23.78%) number of G's = 2,138,195,920 bp (26.18%) number of N's = 1,851,899 bp (0.02%) GC percentage = 52.4% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 35,655,977 number of insertions = 541,566 mapped reads with insertion percentage = 0.64% number of deletions = 465,938 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.97% >>>>>>> Coverage mean coverageData = 2.6388X std coverageData = 34.4485X There is a 10.27% of reference with a coverageData >= 1X There is a 6.79% of reference with a coverageData >= 2X There is a 4.98% of reference with a coverageData >= 3X There is a 4.41% of reference with a coverageData >= 4X There is a 3.97% of reference with a coverageData >= 5X There is a 3.71% of reference with a coverageData >= 6X There is a 3.49% of reference with a coverageData >= 7X There is a 3.31% of reference with a coverageData >= 8X There is a 3.16% of reference with a coverageData >= 9X There is a 3.03% of reference with a coverageData >= 10X There is a 2.92% of reference with a coverageData >= 11X There is a 2.81% of reference with a coverageData >= 12X There is a 2.71% of reference with a coverageData >= 13X There is a 2.63% of reference with a coverageData >= 14X There is a 2.54% of reference with a coverageData >= 15X There is a 2.47% of reference with a coverageData >= 16X There is a 2.39% of reference with a coverageData >= 17X There is a 2.33% of reference with a coverageData >= 18X There is a 2.26% of reference with a coverageData >= 19X There is a 2.2% of reference with a coverageData >= 20X There is a 2.15% of reference with a coverageData >= 21X There is a 2.09% of reference with a coverageData >= 22X There is a 2.04% of reference with a coverageData >= 23X There is a 1.99% of reference with a coverageData >= 24X There is a 1.95% of reference with a coverageData >= 25X There is a 1.9% of reference with a coverageData >= 26X There is a 1.86% of reference with a coverageData >= 27X There is a 1.82% of reference with a coverageData >= 28X There is a 1.78% of reference with a coverageData >= 29X There is a 1.74% of reference with a coverageData >= 30X There is a 1.7% of reference with a coverageData >= 31X There is a 1.67% of reference with a coverageData >= 32X There is a 1.64% of reference with a coverageData >= 33X There is a 1.6% of reference with a coverageData >= 34X There is a 1.57% of reference with a coverageData >= 35X There is a 1.54% of reference with a coverageData >= 36X There is a 1.51% of reference with a coverageData >= 37X There is a 1.48% of reference with a coverageData >= 38X There is a 1.45% of reference with a coverageData >= 39X There is a 1.43% of reference with a coverageData >= 40X There is a 1.4% of reference with a coverageData >= 41X There is a 1.38% of reference with a coverageData >= 42X There is a 1.35% of reference with a coverageData >= 43X There is a 1.33% of reference with a coverageData >= 44X There is a 1.31% of reference with a coverageData >= 45X There is a 1.28% of reference with a coverageData >= 46X There is a 1.26% of reference with a coverageData >= 47X There is a 1.24% of reference with a coverageData >= 48X There is a 1.22% of reference with a coverageData >= 49X There is a 1.2% of reference with a coverageData >= 50X There is a 1.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1316278624 5.280944210766881 47.76271590532087 chr2 243199373 365010659 1.5008700659766914 17.34317997967959 chr3 198022430 359534260 1.8156239169471862 18.475921083003005 chr4 191154276 182700855 0.9557769714761704 17.44512186262484 chr5 180915260 374181161 2.068267546916717 34.59660828972452 chr6 171115067 496663990 2.9025146569939397 31.245143079681764 chr7 159138663 554976535 3.487377137257965 41.38141706843578 chr8 146364022 338466680 2.312499174148139 44.127321139747494 chr9 141213431 211270257 1.4961059688437144 17.354100335339822 chr10 135534747 207583223 1.531586752436259 21.61192500131861 chr11 135006516 488947740 3.6216603056403587 30.467371376161502 chr12 133851895 242786515 1.8138444360462733 18.2138923967741 chr13 115169878 107528607 0.9336521742256252 13.357610947082174 chr14 107349540 237193783 2.2095463380653517 21.475104716130726 chr15 102531392 199974417 1.9503725941807168 17.85498938847094 chr16 90354753 415390022 4.597323419167556 37.04315325909146 chr17 81195210 298342459 3.674384966797918 29.6778318017553 chr18 78077248 108379612 1.3881074804275888 15.34195290893182 chr19 59128983 705245209 11.927233874460516 85.97070377977869 chr20 63025520 221174210 3.5092802090327853 30.933742264489894 chr21 48129895 149220673 3.100373956768449 117.73733559578179 chr22 51304566 112032984 2.183684469721467 20.736726264657072 chrMT 16571 5429 0.32762054191056666 0.6717821795204394 chrX 155270560 466382114 3.0036738065477446 33.328142556303746 chrY 59373566 9492976 0.15988556254141784 7.969466957618504