BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505990.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 = 5,828,064 number of mapped reads = 3,992,195 (68.5%) number of supplementary alignments = 231 (0%) number of secondary alignments = 0 number of mapped bases = 185,284,106 bp number of sequenced bases = 185,243,277 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 287,965 duplication rate = 5.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.73 >>>>>>> ACTG content number of A's = 55,844,986 bp (30.15%) number of C's = 36,009,754 bp (19.44%) number of T's = 56,510,862 bp (30.51%) number of G's = 36,876,888 bp (19.91%) number of N's = 787 bp (0%) GC percentage = 39.35% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 950,891 number of insertions = 9,043 mapped reads with insertion percentage = 0.23% number of deletions = 29,202 mapped reads with deletion percentage = 0.73% homopolymer indels = 46.58% >>>>>>> Coverage mean coverageData = 0.0599X std coverageData = 0.5999X There is a 4.67% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 17775219 0.07131464278277566 1.254000975049416 chr2 243199373 11309584 0.04650334357564318 0.4159522811331578 chr3 198022430 11992854 0.06056310893669975 0.3034713481759245 chr4 191154276 8105819 0.04240459156665687 0.2517185323522119 chr5 180915260 13510193 0.07467691227373523 0.3413068842025663 chr6 171115067 12957032 0.07572116370091478 0.4482417376842266 chr7 159138663 11910666 0.07484457752419348 0.8778372848597414 chr8 146364022 11095107 0.07580487915261033 0.84755954028049 chr9 141213431 8847726 0.06265498924107298 0.4096994627740076 chr10 135534747 5521677 0.04073993660090722 0.5145143144655431 chr11 135006516 9610158 0.07118291979329354 0.4295045936860772 chr12 133851895 5231114 0.039081359288936475 0.2675850591310381 chr13 115169878 6346457 0.05510518123497535 0.2886285259270526 chr14 107349540 6466169 0.06023471549109572 1.0072025856074482 chr15 102531392 5966471 0.05819165119693293 0.29760404954238406 chr16 90354753 5191760 0.05745973319189971 0.34301636937534435 chr17 81195210 2655890 0.032709934489977915 0.2591875069653067 chr18 78077248 5723356 0.07330376193587151 0.675787762324924 chr19 59128983 3790364 0.06410331799550822 0.9210872555212198 chr20 63025520 3900928 0.06189441991117249 0.3234538774916191 chr21 48129895 2646099 0.05497828324786497 0.3059826656745035 chr22 51304566 1061254 0.020685371356615707 0.17292425517903287 chrMT 16571 185976 11.222979904652707 8.265785852863786 chrX 155270560 12976815 0.0835755020140328 0.4051482554868923 chrY 59373566 505418 0.008512508748421814 0.12311066508490401