BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085049.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 = 3,142,090 number of mapped reads = 2,841,307 (90.43%) number of supplementary alignments = 32,521 (1.04%) number of secondary alignments = 0 number of mapped bases = 188,276,762 bp number of sequenced bases = 188,208,674 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,584 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2256 >>>>>>> ACTG content number of A's = 53,530,720 bp (28.44%) number of C's = 35,471,431 bp (18.85%) number of T's = 57,822,358 bp (30.72%) number of G's = 41,358,293 bp (21.97%) number of N's = 25,872 bp (0.01%) GC percentage = 40.82% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,574,397 number of insertions = 15,246 mapped reads with insertion percentage = 0.53% number of deletions = 42,384 mapped reads with deletion percentage = 1.48% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0608X std coverageData = 0.5044X There is a 5.15% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14829012 0.05949438336604987 0.9014431272300966 chr2 243199373 14068772 0.05784871822017403 0.6135570993475618 chr3 198022430 11077149 0.05593886005741875 0.2702204430347382 chr4 191154276 13321767 0.06969117970450214 0.31361664834830916 chr5 180915260 11547233 0.06382674960641795 0.28985837618813737 chr6 171115067 11731326 0.06855811241917113 0.3291456314102171 chr7 159138663 10374065 0.06518884100465265 0.47340143497116 chr8 146364022 11023447 0.07531527795813099 0.8440516803918129 chr9 141213431 9008742 0.06379522072514476 0.49395779502531334 chr10 135534747 8806699 0.06497742604706379 0.44619558834488887 chr11 135006516 6266528 0.046416485556889715 0.44211254358267027 chr12 133851895 8373597 0.06255867352494338 0.29301783398570846 chr13 115169878 5760479 0.050017236277701015 0.25213500930497196 chr14 107349540 6347115 0.059125684190169794 0.31489913339696796 chr15 102531392 5000692 0.048772301852685274 0.25717875233024984 chr16 90354753 5778613 0.06395472078818035 0.3498868152968143 chr17 81195210 5185430 0.06386374270107806 0.361222682598648 chr18 78077248 4839515 0.06198367801078235 0.9887348329412805 chr19 59128983 3570612 0.06038683262994731 0.6592815092916634 chr20 63025520 3588466 0.05693671388986556 0.29381957328140035 chr21 48129895 2714560 0.05640070480103894 0.2910788913419197 chr22 51304566 1682111 0.03278676989490565 0.20457374580586005 chrMT 16571 25073 1.5130649930601654 1.5284806895111567 chrX 155270560 12869322 0.08288320722228348 0.4034033541018294 chrY 59373566 486437 0.008192821027458583 0.15597460392146745