BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085054.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 = 2,193,961 number of mapped reads = 1,939,446 (88.4%) number of supplementary alignments = 36,631 (1.67%) number of secondary alignments = 0 number of mapped bases = 129,260,740 bp number of sequenced bases = 129,224,052 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,938 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1797 >>>>>>> ACTG content number of A's = 37,840,569 bp (29.28%) number of C's = 24,782,559 bp (19.18%) number of T's = 38,187,338 bp (29.55%) number of G's = 28,400,454 bp (21.98%) number of N's = 13,132 bp (0.01%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,220,208 number of insertions = 10,857 mapped reads with insertion percentage = 0.55% number of deletions = 23,416 mapped reads with deletion percentage = 1.2% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.0418X std coverageData = 0.5888X There is a 3.78% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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% 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 11323447 0.045429965047108146 1.259409978036688 chr2 243199373 12568420 0.05167949178882135 0.6409953319881193 chr3 198022430 8080325 0.040805099705119266 0.21619349779615968 chr4 191154276 8038148 0.042050579083043896 0.23090407242396432 chr5 180915260 6824228 0.03772057702595127 0.2125382094448037 chr6 171115067 8792354 0.0513826991050414 0.4700568306995699 chr7 159138663 10643927 0.06688460741937992 0.5745618607682792 chr8 146364022 7847527 0.05361650283154968 0.9913535570814271 chr9 141213431 4319982 0.030591863460919664 0.522896663401003 chr10 135534747 8423226 0.0621480925478099 0.533713680470957 chr11 135006516 5632417 0.04171959374168281 0.6762102641665416 chr12 133851895 5466424 0.04083934710076387 0.23100156645890535 chr13 115169878 2824713 0.024526491206320458 0.1624726060836982 chr14 107349540 4104304 0.038233084184617835 0.2577308535748586 chr15 102531392 2269620 0.022135854743881758 0.1611179702972234 chr16 90354753 3150888 0.03487241008782349 0.2774152302306211 chr17 81195210 2119345 0.02610184763362272 0.27990024759653165 chr18 78077248 3481561 0.04459123610504305 0.9843688272571058 chr19 59128983 1887424 0.03192045430580127 0.8414724093894034 chr20 63025520 2746554 0.04357844251027203 0.23598189177379617 chr21 48129895 1485846 0.030871581997010383 0.21758857929003833 chr22 51304566 773552 0.015077644356254763 0.12710203033819825 chrMT 16571 26610 1.605817391829099 1.6468040863955238 chrX 155270560 6177028 0.03978235152884101 0.34851821323542687 chrY 59373566 252870 0.00425896601864877 0.09506052126127991