BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008692.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,678,111 number of mapped reads = 1,150,859 (68.58%) number of supplementary alignments = 5,567 (0.33%) number of secondary alignments = 0 number of mapped bases = 67,975,186 bp number of sequenced bases = 67,931,577 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,583 duplication rate = 4.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5978 >>>>>>> ACTG content number of A's = 19,049,427 bp (28.04%) number of C's = 11,809,222 bp (17.38%) number of T's = 21,268,183 bp (31.31%) number of G's = 15,779,817 bp (23.23%) number of N's = 24,928 bp (0.04%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 692,996 number of insertions = 5,464 mapped reads with insertion percentage = 0.47% number of deletions = 28,330 mapped reads with deletion percentage = 2.43% homopolymer indels = 48.34% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.1977X There is a 1.85% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.05% 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 5595883 0.022450828718296352 0.23986859729278726 chr2 243199373 5919304 0.024339306170826355 0.23167852264281139 chr3 198022430 5427333 0.027407667909135344 0.1978018845115737 chr4 191154276 3727465 0.019499773052421805 0.16784227390351286 chr5 180915260 3874407 0.021415589818128113 0.17388323267686795 chr6 171115067 4008234 0.02342420261565862 0.19357401398769236 chr7 159138663 3764230 0.023653774193138723 0.2370200676905682 chr8 146364022 4989971 0.034092879737890776 0.2544174139243276 chr9 141213431 2734164 0.019361925991303194 0.18434532211970786 chr10 135534747 3375493 0.024905000929392667 0.2080544009197183 chr11 135006516 2893464 0.02143203221391181 0.1963701101135052 chr12 133851895 3062026 0.022876224501715125 0.18095865550388945 chr13 115169878 2072027 0.01799104970832738 0.1601740860103884 chr14 107349540 2239413 0.02086094639995663 0.171615493484337 chr15 102531392 1852546 0.018068085918505818 0.15912415769158267 chr16 90354753 1673688 0.018523519177790236 0.16577611371119294 chr17 81195210 1650973 0.020333379272003852 0.17614771711420849 chr18 78077248 1332582 0.017067481681731406 0.22597998180123602 chr19 59128983 1085148 0.018352218234499316 0.1865633667319902 chr20 63025520 1459684 0.02316020558021576 0.18335365023577915 chr21 48129895 795518 0.0165285629648683 0.15610168825736784 chr22 51304566 718586 0.014006277725846077 0.13775605542665445 chrMT 16571 43175 2.605455313499487 2.647677388473605 chrX 155270560 3502608 0.022558094721884175 0.18467814861674517 chrY 59373566 177264 0.002985571053623426 0.0746175003777693