BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085137.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 = 2,633,344 number of mapped reads = 2,392,302 (90.85%) number of supplementary alignments = 23,917 (0.91%) number of secondary alignments = 0 number of mapped bases = 161,733,804 bp number of sequenced bases = 161,676,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,982 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.679 >>>>>>> ACTG content number of A's = 45,620,755 bp (28.22%) number of C's = 29,930,792 bp (18.51%) number of T's = 50,880,440 bp (31.47%) number of G's = 35,212,555 bp (21.78%) number of N's = 31,737 bp (0.02%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,363,762 number of insertions = 12,488 mapped reads with insertion percentage = 0.52% number of deletions = 35,613 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.67% >>>>>>> Coverage mean coverageData = 0.0522X std coverageData = 0.3889X There is a 4.53% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 12645179 0.050732788344788116 0.615864764311199 chr2 243199373 14526687 0.059731597252103114 0.4719570122338828 chr3 198022430 11212910 0.056624444008691335 0.2647654184290877 chr4 191154276 10847306 0.05674634241506583 0.27327486961688974 chr5 180915260 10307437 0.05697383957550071 0.2666654541067262 chr6 171115067 9441431 0.055175918553098544 0.29735221527651723 chr7 159138663 9036160 0.056781675990328004 0.49603017640493635 chr8 146364022 8224053 0.05618903394168821 0.6846025579993875 chr9 141213431 6830886 0.048372778365536634 0.347997702185999 chr10 135534747 7397019 0.05457655076450617 0.3575799798924584 chr11 135006516 7293446 0.0540229184197302 0.3400745566191443 chr12 133851895 7478373 0.055870505232667796 0.26757978568857416 chr13 115169878 5315286 0.0461517029652493 0.24204889686035666 chr14 107349540 4822396 0.04492237228030972 0.25108362231727765 chr15 102531392 4570971 0.04458118543830947 0.23954351233375523 chr16 90354753 4355445 0.04820382830331017 0.26355128881651263 chr17 81195210 4018993 0.04949790757361179 0.27024158852854135 chr18 78077248 4297603 0.055042962067515494 0.5905825157113879 chr19 59128983 2692661 0.04553876734189729 0.4754166905545992 chr20 63025520 3095067 0.04910815491883288 0.252225905790503 chr21 48129895 2051046 0.04261480312807663 0.2442409235450201 chr22 51304566 1644937 0.032062195010089355 0.19862678372024606 chrMT 16571 13247 0.7994086053949672 0.9276862039915068 chrX 155270560 9248403 0.05956314577599257 0.2961015794590224 chrY 59373566 366862 0.006178877650704019 0.12460223685607737