BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975206.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 40,867,864 number of mapped reads = 40,814,105 (99.87%) number of supplementary alignments = 250,370 (0.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 20,412,265 number of mapped paired reads (second in pair) = 20,401,840 number of mapped paired reads (both in pair) = 40,776,816 number of mapped paired reads (singletons) = 37,289 number of mapped bases = 3,990,205,459 bp number of sequenced bases = 3,989,716,285 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,045,503 duplication rate = 37.75% >>>>>>> Insert size mean insert size = 240,246.6294 std insert size = 4,829,748.4012 median insert size = 230 >>>>>>> Mapping quality mean mapping quality = 55.9128 >>>>>>> ACTG content number of A's = 1,075,376,207 bp (26.95%) number of C's = 930,129,767 bp (23.31%) number of T's = 1,068,459,375 bp (26.78%) number of G's = 915,527,766 bp (22.95%) number of N's = 223,170 bp (0.01%) GC percentage = 46.26% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 17,086,981 number of insertions = 274,810 mapped reads with insertion percentage = 0.67% number of deletions = 225,773 mapped reads with deletion percentage = 0.54% homopolymer indels = 36.84% >>>>>>> Coverage mean coverageData = 1.289X std coverageData = 9.8254X There is a 10.93% of reference with a coverageData >= 1X There is a 5.69% of reference with a coverageData >= 2X There is a 4.06% of reference with a coverageData >= 3X There is a 3.51% of reference with a coverageData >= 4X There is a 3.21% of reference with a coverageData >= 5X There is a 3.02% of reference with a coverageData >= 6X There is a 2.87% of reference with a coverageData >= 7X There is a 2.74% of reference with a coverageData >= 8X There is a 2.62% of reference with a coverageData >= 9X There is a 2.51% of reference with a coverageData >= 10X There is a 2.42% of reference with a coverageData >= 11X There is a 2.33% of reference with a coverageData >= 12X There is a 2.24% of reference with a coverageData >= 13X There is a 2.17% of reference with a coverageData >= 14X There is a 2.09% of reference with a coverageData >= 15X There is a 2.02% of reference with a coverageData >= 16X There is a 1.96% of reference with a coverageData >= 17X There is a 1.89% of reference with a coverageData >= 18X There is a 1.83% of reference with a coverageData >= 19X There is a 1.77% of reference with a coverageData >= 20X There is a 1.72% of reference with a coverageData >= 21X There is a 1.67% of reference with a coverageData >= 22X There is a 1.62% of reference with a coverageData >= 23X There is a 1.57% of reference with a coverageData >= 24X There is a 1.52% of reference with a coverageData >= 25X There is a 1.48% of reference with a coverageData >= 26X There is a 1.43% of reference with a coverageData >= 27X There is a 1.39% of reference with a coverageData >= 28X There is a 1.35% of reference with a coverageData >= 29X There is a 1.31% of reference with a coverageData >= 30X There is a 1.27% of reference with a coverageData >= 31X There is a 1.24% of reference with a coverageData >= 32X There is a 1.2% of reference with a coverageData >= 33X There is a 1.17% of reference with a coverageData >= 34X There is a 1.14% of reference with a coverageData >= 35X There is a 1.11% of reference with a coverageData >= 36X There is a 1.07% of reference with a coverageData >= 37X There is a 1.05% of reference with a coverageData >= 38X There is a 1.02% of reference with a coverageData >= 39X There is a 0.99% of reference with a coverageData >= 40X There is a 0.96% of reference with a coverageData >= 41X There is a 0.94% of reference with a coverageData >= 42X There is a 0.91% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.86% of reference with a coverageData >= 45X There is a 0.84% of reference with a coverageData >= 46X There is a 0.82% of reference with a coverageData >= 47X There is a 0.79% of reference with a coverageData >= 48X There is a 0.77% of reference with a coverageData >= 49X There is a 0.75% of reference with a coverageData >= 50X There is a 0.73% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 399646825 1.6033934976635424 11.339852876670086 chr2 243199373 311225764 1.27971449992184 9.636513348261134 chr3 198022430 250973646 1.267400091999679 9.59494363321194 chr4 191154276 180949780 0.9466164387554689 8.346062086456785 chr5 180915260 197708743 1.0928251326062821 8.894429576204127 chr6 171115067 226454306 1.3234036602983652 10.281655346295217 chr7 159138663 190985194 1.2001181259138767 9.614984676209824 chr8 146364022 145550617 0.9944425891767309 8.327724804529174 chr9 141213431 155984513 1.1046011126236286 8.82632446148901 chr10 135534747 169765101 1.2525577739854414 9.632821074069332 chr11 135006516 225874682 1.6730650393200281 11.433531995377377 chr12 133851895 218493932 1.6323559109865422 11.0853290482645 chr13 115169878 84439883 0.7331768033999306 7.374903904758973 chr14 107349540 132784498 1.2369358825384813 9.708085368289586 chr15 102531392 139678133 1.3622962711751734 10.03870752270498 chr16 90354753 138962101 1.537961162928529 10.382608236238237 chr17 81195210 199563545 2.457824113023416 13.623736691384936 chr18 78077248 69180465 0.8860515293776748 7.910772437642387 chr19 59128983 183345211 3.1007671990570174 14.791685823702505 chr20 63025520 91557930 1.452712012530797 10.168701402690353 chr21 48129895 42427823 0.8815274373650722 8.100008155805213 chr22 51304566 68289759 1.331065913314616 9.058505004453917 chrMT 16571 320103 19.31705992396355 26.88232614871013 chrX 155270560 164841177 1.0616383234529456 9.449765960993792 chrY 59373566 1201728 0.020240118304499347 0.8017376057024337