BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818995.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,707,223 number of mapped reads = 1,660,104 (97.24%) number of supplementary alignments = 24,636 (1.44%) number of secondary alignments = 0 number of mapped bases = 153,771,918 bp number of sequenced bases = 153,680,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 676,294 duplication rate = 34.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9202 >>>>>>> ACTG content number of A's = 44,107,022 bp (28.7%) number of C's = 31,425,037 bp (20.45%) number of T's = 44,678,713 bp (29.07%) number of G's = 33,462,118 bp (21.77%) number of N's = 7,955 bp (0.01%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 995,835 number of insertions = 25,598 mapped reads with insertion percentage = 1.51% number of deletions = 49,225 mapped reads with deletion percentage = 2.9% homopolymer indels = 40.95% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.5803X There is a 2.5% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% 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 16336625 0.06554296608954086 1.0315407575863296 chr2 243199373 13238951 0.05443661649571769 0.7811838468651834 chr3 198022430 8982205 0.04535953326095433 0.369695461719492 chr4 191154276 8977495 0.04696465696639713 0.4372128249759302 chr5 180915260 5042558 0.027872485715135363 0.30640310241752455 chr6 171115067 6851055 0.04003770749188323 0.41327267775286053 chr7 159138663 3602811 0.022639444947454408 0.444676244537253 chr8 146364022 13458246 0.09195050679872681 0.5836890315771301 chr9 141213431 7013921 0.04966893694410697 0.5535079381940933 chr10 135534747 8748917 0.06455109994782371 0.7479373405920324 chr11 135006516 5634912 0.041738074331167836 0.4376284571651899 chr12 133851895 7459114 0.05572662232387521 0.4201455617521133 chr13 115169878 3461057 0.030051755373049886 0.30088010734793946 chr14 107349540 3740184 0.03484117398174226 0.33807912568336906 chr15 102531392 4274850 0.041693084592082784 0.361475237647658 chr16 90354753 5127461 0.056748104883868146 0.630914521049491 chr17 81195210 5812427 0.07158583615954685 0.5224059013004659 chr18 78077248 3803445 0.04871387116513123 0.6469201877179357 chr19 59128983 3397804 0.057464272639358605 0.9532862386357062 chr20 63025520 4779981 0.0758419922596434 0.512477761845632 chr21 48129895 2239745 0.046535422526893105 0.40974124066443135 chr22 51304566 1292025 0.02518343104198562 0.3083621820274009 chrMT 16571 45668 2.7558988594532616 3.3213226498695603 chrX 155270560 9829675 0.06330675306381325 0.49292966300639995 chrY 59373566 620786 0.010455595677039173 0.581371501497993