BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818915.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 = 2,027,851 number of mapped reads = 1,998,425 (98.55%) number of supplementary alignments = 27,855 (1.37%) number of secondary alignments = 0 number of mapped bases = 185,177,066 bp number of sequenced bases = 185,060,015 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 486,461 duplication rate = 20.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2631 >>>>>>> ACTG content number of A's = 51,537,799 bp (27.85%) number of C's = 37,968,563 bp (20.52%) number of T's = 54,165,827 bp (29.27%) number of G's = 41,385,106 bp (22.36%) number of N's = 2,720 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,130,699 number of insertions = 26,511 mapped reads with insertion percentage = 1.29% number of deletions = 59,740 mapped reads with deletion percentage = 2.92% homopolymer indels = 40.8% >>>>>>> Coverage mean coverageData = 0.0598X std coverageData = 0.7644X There is a 4% of reference with a coverageData >= 1X There is a 1.12% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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% 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 17543970 0.07038686575629434 1.1156950157788386 chr2 243199373 14154333 0.05820053244956351 1.1384398352523801 chr3 198022430 11403874 0.05758879941024863 0.33473169434815775 chr4 191154276 9224995 0.04825942266653768 0.41620916478160747 chr5 180915260 8154992 0.04507630810137298 0.32253277649294065 chr6 171115067 9194879 0.05373506355229373 0.3641528262870362 chr7 159138663 16742618 0.10520773320811423 1.787629440194875 chr8 146364022 15993390 0.10927132078947653 0.6034733395761664 chr9 141213431 6917846 0.048988583812541175 0.6576400132277166 chr10 135534747 8542308 0.06302670118976944 0.9644967784075187 chr11 135006516 8124093 0.06017556219286482 0.43884544558043803 chr12 133851895 7182021 0.05365647606259142 0.33231682488468334 chr13 115169878 5618809 0.04878714033195381 0.30288336518260445 chr14 107349540 5532904 0.051541012658275015 0.351552246801083 chr15 102531392 5136727 0.050099066244999386 0.32007249084830414 chr16 90354753 4676128 0.05175298304451123 0.7650881528745105 chr17 81195210 4726103 0.058206672536471056 0.4646680348824357 chr18 78077248 3563050 0.04563493323945024 0.737346992975227 chr19 59128983 3262919 0.05518307324852856 0.9548940568380854 chr20 63025520 7700495 0.1221805865306625 0.5310909431388444 chr21 48129895 1792196 0.037236648864494716 0.34141475112505726 chr22 51304566 1681918 0.03278300804649629 0.27692051489686037 chrMT 16571 53040 3.200772433769839 2.9050475308604686 chrX 155270560 7572365 0.04876883937302731 0.3746127984187955 chrY 59373566 681093 0.011471317050419374 0.8701768155812969