BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617404.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,309,618 (85.34%) number of supplementary alignments = 391,298 (1.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,327,833 number of mapped paired reads (second in pair) = 12,981,785 number of mapped paired reads (both in pair) = 25,608,472 number of mapped paired reads (singletons) = 1,701,146 number of mapped bases = 2,657,275,179 bp number of sequenced bases = 2,656,705,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,145,404 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 53,933.0669 std insert size = 2,208,737.9922 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 53.5251 >>>>>>> ACTG content number of A's = 793,920,855 bp (29.88%) number of C's = 532,962,606 bp (20.06%) number of T's = 785,463,656 bp (29.57%) number of G's = 543,712,139 bp (20.47%) number of N's = 646,364 bp (0.02%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0161 number of mismatches = 41,599,665 number of insertions = 846,212 mapped reads with insertion percentage = 3.07% number of deletions = 256,162 mapped reads with deletion percentage = 0.92% homopolymer indels = 30.74% >>>>>>> Coverage mean coverageData = 0.8584X std coverageData = 2.6327X There is a 28.25% of reference with a coverageData >= 1X There is a 15.76% of reference with a coverageData >= 2X There is a 9.87% of reference with a coverageData >= 3X There is a 6.7% of reference with a coverageData >= 4X There is a 4.79% of reference with a coverageData >= 5X There is a 3.56% of reference with a coverageData >= 6X There is a 2.72% of reference with a coverageData >= 7X There is a 2.13% of reference with a coverageData >= 8X There is a 1.7% of reference with a coverageData >= 9X There is a 1.38% of reference with a coverageData >= 10X There is a 1.13% of reference with a coverageData >= 11X There is a 0.94% of reference with a coverageData >= 12X There is a 0.79% of reference with a coverageData >= 13X There is a 0.67% of reference with a coverageData >= 14X There is a 0.57% of reference with a coverageData >= 15X There is a 0.49% of reference with a coverageData >= 16X There is a 0.43% of reference with a coverageData >= 17X There is a 0.37% of reference with a coverageData >= 18X There is a 0.33% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.1% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.07% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.06% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 171101073 0.6864619727466998 2.471975922184942 chr2 243199373 265465068 1.0915532582396912 2.79228711793771 chr3 198022430 224832564 1.135389379879845 3.06840155327764 chr4 191154276 128600108 0.6727555914051329 2.078147004432145 chr5 180915260 170618815 0.9430869181516253 2.601252336138607 chr6 171115067 122231388 0.7143227662120484 2.3558629769410366 chr7 159138663 198979124 1.2503506077589706 2.9281475328734246 chr8 146364022 117870950 0.8053273501871928 2.911559717160325 chr9 141213431 106294721 0.752723875110718 2.335846810610023 chr10 135534747 84945607 0.6267441293117255 2.158943990624893 chr11 135006516 196677668 1.4568012998720743 3.447478603076181 chr12 133851895 126336368 0.9438519193172424 2.520762396949328 chr13 115169878 115575568 1.0035225356407862 2.5101977810647536 chr14 107349540 76890078 0.7162590356698315 2.5921582537163403 chr15 102531392 60721135 0.5922199417715893 2.1369476438836794 chr16 90354753 66457405 0.735516426014689 2.9605320611754453 chr17 81195210 81126685 0.9991560462741583 3.260653772738263 chr18 78077248 38214817 0.4894488212494375 1.8079308695764342 chr19 59128983 37548428 0.6350257706952274 2.0855598028319307 chr20 63025520 89688333 1.4230478859991953 4.209789076706824 chr21 48129895 36498117 0.7583252986527397 2.2879300683986488 chr22 51304566 21208544 0.4133851166385464 1.8618482819122435 chrMT 16571 158535 9.56701466417235 4.7776590233680745 chrX 155270560 117105859 0.7542051693508415 2.3157527829110998 chrY 59373566 2128221 0.03584458780865545 0.5260316706580753