BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548927.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,089,646 number of mapped reads = 7,996,127 (87.97%) number of secondary alignments = 0 number of mapped bases = 316,862,948 bp number of sequenced bases = 316,830,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,050 duplication rate = 2.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6054 >>>>>>> ACTG content number of A's = 92,861,475 bp (29.31%) number of C's = 65,105,995 bp (20.55%) number of T's = 93,544,809 bp (29.53%) number of G's = 65,315,337 bp (20.62%) number of N's = 2,710 bp (0%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 861,049 number of insertions = 9,228 mapped reads with insertion percentage = 0.12% number of deletions = 24,590 mapped reads with deletion percentage = 0.31% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.1024X std coverageData = 0.8996X There is a 8.24% of reference with a coverageData >= 1X There is a 1.45% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 24839215 0.09965557919312065 1.0790725308017077 chr2 243199373 26776053 0.11009918598762176 0.6026744306731958 chr3 198022430 21715240 0.10966050664058612 0.3933974255040286 chr4 191154276 21115836 0.11046488962663854 0.40952975947810843 chr5 180915260 19881833 0.1098958318938933 0.4030026962377547 chr6 171115067 18675838 0.10914198455709338 0.4512096888183891 chr7 159138663 17671350 0.11104372543333482 0.9603115078981629 chr8 146364022 16516977 0.11284861384855904 3.084127009710843 chr9 141213431 13234506 0.09371988136170985 0.5963000818637753 chr10 135534747 14491786 0.10692303133158909 0.5416184736777072 chr11 135006516 14281504 0.10578381268649285 0.6357179333686872 chr12 133851895 14462697 0.10804999809677704 0.40759711953325445 chr13 115169878 10400051 0.09030183222040054 0.35299961064213653 chr14 107349540 9816906 0.09144804905545008 0.4332500929037379 chr15 102531392 9043889 0.08820604912883656 0.35365383537677725 chr16 90354753 8518271 0.09427584844374484 0.41218077900248185 chr17 81195210 7915474 0.09748695766659142 0.4064692393318839 chr18 78077248 8433809 0.10801877904303185 1.0934619794594178 chr19 59128983 5860525 0.09911425332649472 0.9830581423958386 chr20 63025520 6201408 0.09839518975805356 0.3905729920982504 chr21 48129895 4073066 0.08462652993529282 0.4052173634170059 chr22 51304566 3247006 0.06328883086156503 0.3315483571332577 chrMT 16571 9648 0.5822219540160521 1.031070114636161 chrX 155270560 18715788 0.12053661685769665 0.5129872412747466 chrY 59373566 964272 0.016240762766379906 0.20988948141703942