BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080714.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,399,528 number of mapped reads = 2,227,306 (92.82%) number of supplementary alignments = 13,392 (0.56%) number of secondary alignments = 0 number of mapped bases = 153,022,505 bp number of sequenced bases = 152,965,417 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,421 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7098 >>>>>>> ACTG content number of A's = 43,130,025 bp (28.2%) number of C's = 28,848,363 bp (18.86%) number of T's = 48,044,830 bp (31.41%) number of G's = 32,939,956 bp (21.53%) number of N's = 2,243 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,205,936 number of insertions = 10,842 mapped reads with insertion percentage = 0.48% number of deletions = 32,545 mapped reads with deletion percentage = 1.45% homopolymer indels = 49.03% >>>>>>> Coverage mean coverageData = 0.0494X std coverageData = 0.3808X There is a 4.02% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 19940328 0.08000111662710763 0.5628279191486708 chr2 243199373 10290492 0.042312987377644266 0.3780454386658843 chr3 198022430 9619403 0.04857734045582614 0.2579493984300881 chr4 191154276 5821474 0.03045432266448489 0.20922216391518605 chr5 180915260 6557109 0.03624409018896471 0.22186516476969304 chr6 171115067 9025928 0.052747710404718484 0.33618443169472567 chr7 159138663 9528244 0.059873847249803776 0.9095646000522852 chr8 146364022 17537291 0.119819684922296 0.5168953952086018 chr9 141213431 5046682 0.03573797452736631 0.26355455389762283 chr10 135534747 7415153 0.054710346712787974 0.3380920824687234 chr11 135006516 6737303 0.049903539470643035 0.30114659222160123 chr12 133851895 5080060 0.037952843327320844 0.22828672361443117 chr13 115169878 2937367 0.02550464627565204 0.1873221376801122 chr14 107349540 2978806 0.02774866105620946 0.20208932001713695 chr15 102531392 2911960 0.028400667768169966 0.19624049430500537 chr16 90354753 4331457 0.047938341439547734 0.2670053832047686 chr17 81195210 2982335 0.03673043028030841 0.23388787676706282 chr18 78077248 4876913 0.06246266518000224 0.4065456972935383 chr19 59128983 2645715 0.044744808142565214 0.36020770309298666 chr20 63025520 4088876 0.06487651351389088 0.30299918062201886 chr21 48129895 2154220 0.04475846041218249 0.2548376457453606 chr22 51304566 1811070 0.035300366832846805 0.2204845127757772 chrMT 16571 12961 0.7821495383501298 1.038459170747835 chrX 155270560 8426256 0.054268214141818 0.2869590789148092 chrY 59373566 265102 0.004464983625878223 0.09268243373975789