BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3087911.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,894,225 number of mapped reads = 1,701,015 (89.8%) number of supplementary alignments = 16,982 (0.9%) number of secondary alignments = 0 number of mapped bases = 112,136,517 bp number of sequenced bases = 112,095,596 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,095 duplication rate = 3.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1677 >>>>>>> ACTG content number of A's = 29,820,389 bp (26.6%) number of C's = 20,916,044 bp (18.66%) number of T's = 35,245,199 bp (31.44%) number of G's = 26,108,389 bp (23.29%) number of N's = 5,575 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 786,556 number of insertions = 8,370 mapped reads with insertion percentage = 0.49% number of deletions = 25,162 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.86% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.2933X There is a 3.06% of reference with a coverageData >= 1X There is a 0.43% 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% 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 11911077 0.04778755195157568 0.4989614727490047 chr2 243199373 9886065 0.04065004312326085 0.4518296646116991 chr3 198022430 7234103 0.036531735319074714 0.2229529655423614 chr4 191154276 5326811 0.027866554238106606 0.19699771501649999 chr5 180915260 5198530 0.028734613100077903 0.19613141876529133 chr6 171115067 6970931 0.04073826532177906 0.2623899020696732 chr7 159138663 8099109 0.050893408599266665 0.31558966734045407 chr8 146364022 7623920 0.052088757167386396 0.2947510957331773 chr9 141213431 4870458 0.034490047904862535 0.25795812925527417 chr10 135534747 5558389 0.0410108044101783 0.2599667660732561 chr11 135006516 4038229 0.02991136368558685 0.23634223338775415 chr12 133851895 4185283 0.03126801454697373 0.20412392490188833 chr13 115169878 3847733 0.03340919576210717 0.21068721246548036 chr14 107349540 2706626 0.025213205384950883 0.18463439238931553 chr15 102531392 3202522 0.03123455107290458 0.21324481097895123 chr16 90354753 3289669 0.0364083669178975 0.2296868912977329 chr17 81195210 2163519 0.02664589450535321 0.19649887720520884 chr18 78077248 3967153 0.05081061514873065 0.45246364759340757 chr19 59128983 2704096 0.04573215811947924 0.35422276342973474 chr20 63025520 1945597 0.03086998726864927 0.20503190891757722 chr21 48129895 1601382 0.033272085883420274 0.21607844924519515 chr22 51304566 1095078 0.02134464990893793 0.16721272688718986 chrMT 16571 6325 0.38169090579928794 0.6677375364428341 chrX 155270560 4493939 0.028942634070489602 0.204218220050586 chrY 59373566 209973 0.00353647277982259 0.08826912222846602