BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504662.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 = 99,278,696 number of mapped reads = 98,499,628 (99.22%) number of supplementary alignments = 1,176,251 (1.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 49,467,961 number of mapped paired reads (second in pair) = 49,031,667 number of mapped paired reads (both in pair) = 98,031,450 number of mapped paired reads (singletons) = 468,178 number of mapped bases = 9,255,514,762 bp number of sequenced bases = 9,253,351,102 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,098,614 duplication rate = 22.52% >>>>>>> Insert size mean insert size = 24,295.7286 std insert size = 1,487,080.3455 median insert size = 133 >>>>>>> Mapping quality mean mapping quality = 53.086 >>>>>>> ACTG content number of A's = 2,705,593,029 bp (29.24%) number of C's = 1,857,095,956 bp (20.07%) number of T's = 2,753,556,744 bp (29.76%) number of G's = 1,860,021,087 bp (20.1%) number of N's = 77,084,286 bp (0.83%) GC percentage = 40.17% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 90,899,920 number of insertions = 901,898 mapped reads with insertion percentage = 0.91% number of deletions = 1,164,312 mapped reads with deletion percentage = 1.16% homopolymer indels = 50.8% >>>>>>> Coverage mean coverageData = 2.9898X std coverageData = 436.5112X There is a 31.15% of reference with a coverageData >= 1X There is a 23.16% of reference with a coverageData >= 2X There is a 16.28% of reference with a coverageData >= 3X There is a 12.97% of reference with a coverageData >= 4X There is a 10.5% of reference with a coverageData >= 5X There is a 8.81% of reference with a coverageData >= 6X There is a 7.52% of reference with a coverageData >= 7X There is a 6.52% of reference with a coverageData >= 8X There is a 5.73% of reference with a coverageData >= 9X There is a 5.08% of reference with a coverageData >= 10X There is a 4.55% of reference with a coverageData >= 11X There is a 4.1% of reference with a coverageData >= 12X There is a 3.72% of reference with a coverageData >= 13X There is a 3.39% of reference with a coverageData >= 14X There is a 3.11% of reference with a coverageData >= 15X There is a 2.86% of reference with a coverageData >= 16X There is a 2.64% of reference with a coverageData >= 17X There is a 2.45% of reference with a coverageData >= 18X There is a 2.28% of reference with a coverageData >= 19X There is a 2.13% of reference with a coverageData >= 20X There is a 1.99% of reference with a coverageData >= 21X There is a 1.87% of reference with a coverageData >= 22X There is a 1.76% of reference with a coverageData >= 23X There is a 1.65% of reference with a coverageData >= 24X There is a 1.56% of reference with a coverageData >= 25X There is a 1.48% of reference with a coverageData >= 26X There is a 1.4% of reference with a coverageData >= 27X There is a 1.33% of reference with a coverageData >= 28X There is a 1.26% of reference with a coverageData >= 29X There is a 1.2% of reference with a coverageData >= 30X There is a 1.14% of reference with a coverageData >= 31X There is a 1.09% of reference with a coverageData >= 32X There is a 1.04% of reference with a coverageData >= 33X There is a 0.99% of reference with a coverageData >= 34X There is a 0.95% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.84% of reference with a coverageData >= 38X There is a 0.81% of reference with a coverageData >= 39X There is a 0.78% of reference with a coverageData >= 40X There is a 0.75% of reference with a coverageData >= 41X There is a 0.72% of reference with a coverageData >= 42X There is a 0.69% of reference with a coverageData >= 43X There is a 0.67% of reference with a coverageData >= 44X There is a 0.65% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.58% of reference with a coverageData >= 48X There is a 0.57% of reference with a coverageData >= 49X There is a 0.55% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 511006095 2.0501697967685306 15.061204612120696 chr2 243199373 600605875 2.469602892438378 11.256981297389006 chr3 198022430 581579789 2.936938956864634 54.21891769816282 chr4 191154276 592332311 3.0987133711829706 30.817142425711474 chr5 180915260 513136742 2.8363375317261794 19.602276749087157 chr6 171115067 511602041 2.9898129368116955 29.178620076527523 chr7 159138663 333146181 2.0934333286437123 8.939540136568928 chr8 146364022 402566351 2.750446082986159 19.91822872647679 chr9 141213431 2327569846 16.482637873163778 2040.9514248589055 chr10 135534747 353767532 2.610161156681098 40.54585066470475 chr11 135006516 334305771 2.47621952558201 13.986287959232643 chr12 133851895 308906287 2.3078215441029055 10.988491350497076 chr13 115169878 229097976 1.9892178404495662 8.490553655791844 chr14 107349540 261657933 2.4374387910744657 32.9271235316032 chr15 102531392 193817071 1.8903193180094542 9.277630946504775 chr16 90354753 165369429 1.8302239064280326 16.391365788765963 chr17 81195210 111316614 1.3709751351095711 6.141334652353268 chr18 78077248 167432433 2.1444458826212727 9.283376945821772 chr19 59128983 78986747 1.3358380779185735 7.715915223348536 chr20 63025520 101505182 1.610540968166546 6.727440381801159 chr21 48129895 66288239 1.3772778644125445 6.225557922293315 chr22 51304566 52369737 1.0207617193370275 5.3748959482329886 chrMT 16571 2896 0.1747631404260455 0.6312849319749474 chrX 155270560 450183963 2.8993517058224043 13.893832882086212 chrY 59373566 6961721 0.11725286973667709 1.3780148282351579