BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549126.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,975,444 number of mapped reads = 7,859,224 (56.24%) number of secondary alignments = 0 number of mapped bases = 311,918,620 bp number of sequenced bases = 311,890,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 385,653 duplication rate = 3.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4583 >>>>>>> ACTG content number of A's = 92,252,818 bp (29.58%) number of C's = 62,967,372 bp (20.19%) number of T's = 93,166,083 bp (29.87%) number of G's = 63,490,820 bp (20.36%) number of N's = 12,965 bp (0%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 948,211 number of insertions = 7,912 mapped reads with insertion percentage = 0.1% number of deletions = 22,799 mapped reads with deletion percentage = 0.29% homopolymer indels = 44.47% >>>>>>> Coverage mean coverageData = 0.1008X std coverageData = 1.0519X There is a 7.4% of reference with a coverageData >= 1X There is a 1.8% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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% 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 24964999 0.10016022788565089 1.204765401802924 chr2 243199373 27046348 0.1112105992148261 0.6090753868936813 chr3 198022430 21894406 0.11056528293284755 0.4287688790236994 chr4 191154276 21850522 0.11430830875057171 0.4813496538862048 chr5 180915260 20010012 0.1106043348692642 0.4349195500956749 chr6 171115067 18913449 0.11053058816848665 0.4748709084794819 chr7 159138663 17545681 0.11025404304169628 0.9123070146683546 chr8 146364022 16898653 0.11545633120139319 3.891902880484391 chr9 141213431 13218590 0.09360717253587586 0.5629859688727015 chr10 135534747 14631072 0.10795070875810171 0.627133926536885 chr11 135006516 14434727 0.10691874309237044 0.5446819774610988 chr12 133851895 14382270 0.10744913249080261 0.4410841360708978 chr13 115169878 10504376 0.09120766803278198 0.38726070554124914 chr14 107349540 9803422 0.09132244069234018 0.4916196527972862 chr15 102531392 8860543 0.0864178553237627 0.3773101970052231 chr16 90354753 8276985 0.09160541892024208 0.4332490077501981 chr17 81195210 7414474 0.09131664293989757 0.4176218577341309 chr18 78077248 8490717 0.10874764694575301 1.1085790076664523 chr19 59128983 5304856 0.08971667921296736 0.9492005458069736 chr20 63025520 6292233 0.09983627267176852 0.4356352665807052 chr21 48129895 4174918 0.08674271988334901 0.45934517376443057 chr22 51304566 3212602 0.06261824727257219 0.3427213821523111 chrMT 16571 44009 2.6557842013155515 3.2738217032590415 chrX 155270560 10985437 0.07075028904384707 0.4130253668005707 chrY 59373566 2763319 0.04654123351795983 0.4578018881831835