BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549044.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 = 4,441,396 number of mapped reads = 3,730,009 (83.98%) number of secondary alignments = 0 number of mapped bases = 147,319,123 bp number of sequenced bases = 147,305,928 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,118 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.0697 >>>>>>> ACTG content number of A's = 40,233,667 bp (27.31%) number of C's = 32,879,486 bp (22.32%) number of T's = 41,297,197 bp (28.03%) number of G's = 32,894,444 bp (22.33%) number of N's = 1,134 bp (0%) GC percentage = 44.65% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 437,799 number of insertions = 5,147 mapped reads with insertion percentage = 0.14% number of deletions = 10,268 mapped reads with deletion percentage = 0.28% homopolymer indels = 38.22% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.3408X There is a 4.08% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12245225 0.04912816245300348 0.4472822230527528 chr2 243199373 12127843 0.04986790405911121 0.34946456854706737 chr3 198022430 9839859 0.04969062848082412 0.25345303658722734 chr4 191154276 9145271 0.047842356401172 0.2730286218168981 chr5 180915260 8472707 0.046832461783489134 0.2471099911569633 chr6 171115067 8269422 0.04832667365288178 0.2562963461815199 chr7 159138663 8576658 0.053894244417524106 0.38205337326173605 chr8 146364022 7548438 0.05157304299823081 0.6550173448081893 chr9 141213431 5999451 0.04248498855608147 0.3341548501947016 chr10 135534747 7437355 0.054874157104524646 0.34432657606666955 chr11 135006516 7121205 0.05274712073897233 0.29549235665273094 chr12 133851895 6549903 0.04893395793910874 0.2543006153679064 chr13 115169878 4688054 0.04070555670815246 0.22876989562445937 chr14 107349540 4684157 0.04363462572825184 0.2513120204531808 chr15 102531392 4618874 0.04504838869250893 0.24235214218720946 chr16 90354753 4489733 0.049690058916989126 0.27504034567488866 chr17 81195210 4506573 0.055502941614412965 0.27205889790949955 chr18 78077248 4033749 0.05166356529369478 0.533365348242108 chr19 59128983 3602401 0.06092445391797116 0.4881504988052685 chr20 63025520 3051781 0.04842135376272976 0.25845894635591277 chr21 48129895 1874202 0.03894049633808676 0.26724382259314 chr22 51304566 1977416 0.03854269033286433 0.30606145181768524 chrMT 16571 2709 0.16347836581980568 0.4302432137467359 chrX 155270560 5262351 0.03389149237305514 0.23567813879144917 chrY 59373566 1193786 0.02010635507390612 0.2319463749420853