BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926908.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 26,974,058 number of mapped reads = 25,218,204 (93.49%) number of supplementary alignments = 226,512 (0.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,678,178 number of mapped paired reads (second in pair) = 12,540,026 number of mapped paired reads (both in pair) = 24,920,456 number of mapped paired reads (singletons) = 297,748 number of mapped bases = 2,366,820,965 bp number of sequenced bases = 2,364,976,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,640,374 duplication rate = 5.23% >>>>>>> Insert size mean insert size = 100,558.8331 std insert size = 3,127,457.6297 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 53.5154 >>>>>>> ACTG content number of A's = 674,572,027 bp (28.52%) number of C's = 472,812,916 bp (19.99%) number of T's = 680,166,543 bp (28.76%) number of G's = 537,201,606 bp (22.71%) number of N's = 223,518 bp (0.01%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 24,548,634 number of insertions = 383,649 mapped reads with insertion percentage = 1.5% number of deletions = 1,304,164 mapped reads with deletion percentage = 5.03% homopolymer indels = 53.02% >>>>>>> Coverage mean coverageData = 0.7646X std coverageData = 2.6402X There is a 30.98% of reference with a coverageData >= 1X There is a 16.91% of reference with a coverageData >= 2X There is a 9.77% of reference with a coverageData >= 3X There is a 6.02% of reference with a coverageData >= 4X There is a 3.84% of reference with a coverageData >= 5X There is a 2.51% of reference with a coverageData >= 6X There is a 1.68% of reference with a coverageData >= 7X There is a 1.14% of reference with a coverageData >= 8X There is a 0.79% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 197479778 0.7922940260196984 2.6630487942062286 chr2 243199373 203322043 0.8360302927261247 3.60985817449381 chr3 198022430 160632485 0.8111832836310513 1.7202610124653674 chr4 191154276 139369661 0.7290951785980451 1.809744553184779 chr5 180915260 144001074 0.7959586935894739 1.6729296917839496 chr6 171115067 132185297 0.7724936168245196 1.6661316030964413 chr7 159138663 121616777 0.7642189189436636 1.757801206076412 chr8 146364022 122600453 0.8376406395828614 1.907428890932641 chr9 141213431 101535326 0.7190203175503894 2.5449208860560404 chr10 135534747 119620122 0.8825790038918949 7.004912868799218 chr11 135006516 113670543 0.8419633834562474 2.0234944552880916 chr12 133851895 104858497 0.7833919497366847 1.7385017279999133 chr13 115169878 70995410 0.6164407849767801 1.4691548401536063 chr14 107349540 71631973 0.6672778756201471 1.596798261363439 chr15 102531392 70804729 0.6905663486944564 1.6614385878224054 chr16 90354753 75536803 0.836002539899589 4.436899754886512 chr17 81195210 63138369 0.7776119921359893 1.9246066964099597 chr18 78077248 62919814 0.8058661852425946 2.6536787621436204 chr19 59128983 39034196 0.6601533464561702 1.8729143013929006 chr20 63025520 56241295 0.8923574926474228 1.922242669439448 chr21 48129895 29940377 0.6220744300397912 2.2989730022373216 chr22 51304566 31279918 0.6096907242135134 1.6467618481096347 chrMT 16571 1568 0.0946231368052622 0.4083811266690427 chrX 155270560 131096876 0.8443125084368859 1.7883294460406542 chrY 59373566 3307581 0.05570797280392423 1.2466334083035175