BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504412.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 134,778,550 number of mapped reads = 128,946,101 (95.67%) number of supplementary alignments = 2,105,090 (1.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 64,527,675 number of mapped paired reads (second in pair) = 64,418,426 number of mapped paired reads (both in pair) = 128,623,964 number of mapped paired reads (singletons) = 322,137 number of mapped bases = 12,337,610,237 bp number of sequenced bases = 12,333,529,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,371,467 duplication rate = 28.09% >>>>>>> Insert size mean insert size = 79,659.0344 std insert size = 2,703,298.9183 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 50.5494 >>>>>>> ACTG content number of A's = 3,685,249,172 bp (29.88%) number of C's = 2,473,401,403 bp (20.05%) number of T's = 3,690,108,582 bp (29.92%) number of G's = 2,482,797,309 bp (20.13%) number of N's = 1,973,424 bp (0.02%) GC percentage = 40.18% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 64,218,747 number of insertions = 1,202,112 mapped reads with insertion percentage = 0.92% number of deletions = 2,409,682 mapped reads with deletion percentage = 1.84% homopolymer indels = 46.87% >>>>>>> Coverage mean coverageData = 3.9854X std coverageData = 47.0456X There is a 27.67% of reference with a coverageData >= 1X There is a 21.28% of reference with a coverageData >= 2X There is a 16.58% of reference with a coverageData >= 3X There is a 13.96% of reference with a coverageData >= 4X There is a 11.96% of reference with a coverageData >= 5X There is a 10.52% of reference with a coverageData >= 6X There is a 9.36% of reference with a coverageData >= 7X There is a 8.44% of reference with a coverageData >= 8X There is a 7.68% of reference with a coverageData >= 9X There is a 7.04% of reference with a coverageData >= 10X There is a 6.49% of reference with a coverageData >= 11X There is a 6.02% of reference with a coverageData >= 12X There is a 5.61% of reference with a coverageData >= 13X There is a 5.25% of reference with a coverageData >= 14X There is a 4.93% of reference with a coverageData >= 15X There is a 4.64% of reference with a coverageData >= 16X There is a 4.38% of reference with a coverageData >= 17X There is a 4.15% of reference with a coverageData >= 18X There is a 3.94% of reference with a coverageData >= 19X There is a 3.75% of reference with a coverageData >= 20X There is a 3.57% of reference with a coverageData >= 21X There is a 3.41% of reference with a coverageData >= 22X There is a 3.26% of reference with a coverageData >= 23X There is a 3.12% of reference with a coverageData >= 24X There is a 2.99% of reference with a coverageData >= 25X There is a 2.87% of reference with a coverageData >= 26X There is a 2.76% of reference with a coverageData >= 27X There is a 2.66% of reference with a coverageData >= 28X There is a 2.56% of reference with a coverageData >= 29X There is a 2.47% of reference with a coverageData >= 30X There is a 2.39% of reference with a coverageData >= 31X There is a 2.3% of reference with a coverageData >= 32X There is a 2.23% of reference with a coverageData >= 33X There is a 2.16% of reference with a coverageData >= 34X There is a 2.09% of reference with a coverageData >= 35X There is a 2.02% of reference with a coverageData >= 36X There is a 1.96% of reference with a coverageData >= 37X There is a 1.91% of reference with a coverageData >= 38X There is a 1.85% of reference with a coverageData >= 39X There is a 1.8% of reference with a coverageData >= 40X There is a 1.75% of reference with a coverageData >= 41X There is a 1.7% of reference with a coverageData >= 42X There is a 1.65% of reference with a coverageData >= 43X There is a 1.61% of reference with a coverageData >= 44X There is a 1.57% of reference with a coverageData >= 45X There is a 1.53% of reference with a coverageData >= 46X There is a 1.49% of reference with a coverageData >= 47X There is a 1.46% of reference with a coverageData >= 48X There is a 1.42% of reference with a coverageData >= 49X There is a 1.39% of reference with a coverageData >= 50X There is a 1.35% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1228025263 4.926869421922122 86.05924498552893 chr2 243199373 1052867667 4.3292367657543265 24.772252440736306 chr3 198022430 841039590 4.24719356287063 22.24768950043852 chr4 191154276 786911007 4.11662780172388 24.195140193052925 chr5 180915260 835515356 4.618269105657533 37.876346368793605 chr6 171115067 792195883 4.629609168197912 37.26423494347094 chr7 159138663 937256824 5.889560753693149 84.98370811288335 chr8 146364022 842959740 5.759337086268372 79.62277864046428 chr9 141213431 471434693 3.3384550581452834 21.45899977407533 chr10 135534747 550200918 4.059482384985748 38.801825693372 chr11 135006516 648043614 4.80009138225595 35.69689220152096 chr12 133851895 649290329 4.850811630272399 60.32148946296207 chr13 115169878 407856541 3.541347339101983 44.70697080827229 chr14 107349540 409224017 3.812070522146625 47.83807809659234 chr15 102531392 359708198 3.5082738172519887 54.036564710754924 chr16 90354753 288473193 3.1926731402829467 39.05549143090715 chr17 81195210 185822654 2.288591334390292 14.849776210540279 chr18 78077248 337088736 4.317374710748002 35.062093939829886 chr19 59128983 101310717 1.713385075471364 10.181463881898821 chr20 63025520 194329732 3.083349919207331 21.659399462656822 chr21 48129895 147624306 3.0672060680788937 23.148035434047266 chr22 51304566 91162024 1.7768793522198394 14.783312400905242 chrMT 16571 1134 0.06843280429666285 0.47428179176889224 chrX 155270560 20940974 0.1348676400729153 1.848829541164611 chrY 59373566 158327127 2.6666265421888253 25.50942102951019