BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514771.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 47,136,964 number of mapped reads = 46,350,835 (98.33%) number of supplementary alignments = 3,535,052 (7.5%) number of secondary alignments = 0 number of mapped bases = 4,354,835,845 bp number of sequenced bases = 4,349,027,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,423,560 duplication rate = 49.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.5753 >>>>>>> ACTG content number of A's = 1,257,385,025 bp (28.91%) number of C's = 912,323,050 bp (20.98%) number of T's = 1,246,110,226 bp (28.65%) number of G's = 929,556,120 bp (21.37%) number of N's = 3,652,927 bp (0.08%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 32,358,075 number of insertions = 2,599,083 mapped reads with insertion percentage = 5.1% number of deletions = 2,314,315 mapped reads with deletion percentage = 4.41% homopolymer indels = 34.47% >>>>>>> Coverage mean coverageData = 1.4067X std coverageData = 119.5932X There is a 2.94% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 1.37% of reference with a coverageData >= 3X There is a 1.21% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 1.03% of reference with a coverageData >= 6X There is a 0.96% of reference with a coverageData >= 7X There is a 0.91% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.83% of reference with a coverageData >= 10X There is a 0.8% of reference with a coverageData >= 11X There is a 0.77% of reference with a coverageData >= 12X There is a 0.74% of reference with a coverageData >= 13X There is a 0.71% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.67% of reference with a coverageData >= 16X There is a 0.65% of reference with a coverageData >= 17X There is a 0.63% of reference with a coverageData >= 18X There is a 0.62% of reference with a coverageData >= 19X There is a 0.6% of reference with a coverageData >= 20X There is a 0.59% of reference with a coverageData >= 21X There is a 0.57% of reference with a coverageData >= 22X There is a 0.56% of reference with a coverageData >= 23X There is a 0.55% of reference with a coverageData >= 24X There is a 0.53% of reference with a coverageData >= 25X There is a 0.52% of reference with a coverageData >= 26X There is a 0.51% of reference with a coverageData >= 27X There is a 0.5% of reference with a coverageData >= 28X There is a 0.49% of reference with a coverageData >= 29X There is a 0.48% of reference with a coverageData >= 30X There is a 0.48% of reference with a coverageData >= 31X There is a 0.47% of reference with a coverageData >= 32X There is a 0.46% of reference with a coverageData >= 33X There is a 0.45% of reference with a coverageData >= 34X There is a 0.44% of reference with a coverageData >= 35X There is a 0.44% of reference with a coverageData >= 36X There is a 0.43% of reference with a coverageData >= 37X There is a 0.42% of reference with a coverageData >= 38X There is a 0.42% of reference with a coverageData >= 39X There is a 0.41% of reference with a coverageData >= 40X There is a 0.4% of reference with a coverageData >= 41X There is a 0.4% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.39% of reference with a coverageData >= 44X There is a 0.38% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.37% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.36% of reference with a coverageData >= 49X There is a 0.36% of reference with a coverageData >= 50X There is a 0.35% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 386196039 1.5494285929983702 48.282414227143725 chr2 243199373 435821007 1.7920317870227405 141.1115332971992 chr3 198022430 239406864 1.2089886181075549 53.63200148832404 chr4 191154276 338603354 1.7713616513606005 184.03780714629647 chr5 180915260 233295789 1.2895307394191071 56.841010051325554 chr6 171115067 337627349 1.9731012290110024 62.16761408007522 chr7 159138663 200291994 1.2586004571371823 58.02764334711134 chr8 146364022 176004860 1.2025145086543194 82.50132879717886 chr9 141213431 193555420 1.3706587158837604 107.30229618008987 chr10 135534747 160843531 1.1867328088198668 40.810639930091206 chr11 135006516 265165877 1.9640968810720216 65.89111230187869 chr12 133851895 171631242 1.282247382452075 34.221814704319904 chr13 115169878 296457480 2.5740886866268973 455.8221091788465 chr14 107349540 76018919 0.7081438728102608 23.385432570480383 chr15 102531392 95661821 0.9330003146743585 51.88964734364404 chr16 90354753 148969138 1.6487139088300091 59.91051164584474 chr17 81195210 95951354 1.1817366320008287 81.9039982474851 chr18 78077248 131948584 1.689974831080112 56.486008520603136 chr19 59128983 73782651 1.247825469956079 62.42701348504589 chr20 63025520 133533449 2.11872030567935 64.94545552609002 chr21 48129895 49637264 1.0313187676806692 92.58462232533006 chr22 51304566 25080136 0.48884802962761637 16.795416886845803 chrMT 16571 1799002 108.56327318809969 199.427824273593 chrX 155270560 69938021 0.4504267969407723 28.22199477155849 chrY 59373566 17614700 0.29667579676787476 9.524310229241836