BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819024.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 = 1,762,259 number of mapped reads = 1,634,210 (92.73%) number of supplementary alignments = 25,178 (1.43%) number of secondary alignments = 0 number of mapped bases = 151,314,634 bp number of sequenced bases = 151,220,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 604,505 duplication rate = 29.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.206 >>>>>>> ACTG content number of A's = 42,579,017 bp (28.16%) number of C's = 31,152,622 bp (20.6%) number of T's = 44,255,790 bp (29.27%) number of G's = 33,226,010 bp (21.97%) number of N's = 6,765 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 944,396 number of insertions = 25,877 mapped reads with insertion percentage = 1.54% number of deletions = 49,886 mapped reads with deletion percentage = 2.98% homopolymer indels = 41.37% >>>>>>> Coverage mean coverageData = 0.0489X std coverageData = 0.5861X There is a 2.68% of reference with a coverageData >= 1X There is a 1% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% 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% 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 15523586 0.06228103239108881 1.0413340919714216 chr2 243199373 12651082 0.05201938575721575 0.8569893311721981 chr3 198022430 8520493 0.04302791860497823 0.3475005615273613 chr4 191154276 8405611 0.04397291641019843 0.41957381439720326 chr5 180915260 8049556 0.04449351591457791 0.361442204316253 chr6 171115067 6297476 0.0368025803361898 0.3777043264826057 chr7 159138663 7704782 0.048415525521915435 0.6555919773262021 chr8 146364022 14101237 0.09634360143505759 0.5763734058263513 chr9 141213431 6291935 0.04455620797146413 0.5267447023829104 chr10 135534747 7300384 0.05386356016881782 0.7393822142734058 chr11 135006516 5100639 0.03778068756325806 0.35908410891788217 chr12 133851895 7217927 0.05392472777467962 0.40412055024446514 chr13 115169878 3048478 0.026469403744614543 0.269951927780794 chr14 107349540 3457057 0.032203743024888605 0.32118486522520523 chr15 102531392 4100199 0.03998969408315455 0.33627139114722904 chr16 90354753 4694535 0.051956702266675446 0.7071288644479083 chr17 81195210 5281752 0.06505004420827287 0.4926433529180626 chr18 78077248 3481712 0.04459317008714241 0.5702450603604063 chr19 59128983 3056042 0.05168433219965918 0.7849789538346332 chr20 63025520 4097310 0.06501033232252586 0.4593161491305822 chr21 48129895 2126349 0.04417938165042745 0.3819109477877279 chr22 51304566 1177476 0.022950705790981643 0.284714643577165 chrMT 16571 65212 3.9353086717759944 3.635320248287236 chrX 155270560 8980229 0.05783600574378041 0.4379600882603414 chrY 59373566 583575 0.00982886896165206 0.6639797513817597