BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008806.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 = 1,272,521 number of mapped reads = 1,086,800 (85.41%) number of supplementary alignments = 12,773 (1%) number of secondary alignments = 0 number of mapped bases = 71,657,745 bp number of sequenced bases = 71,620,912 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,278 duplication rate = 7.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0774 >>>>>>> ACTG content number of A's = 19,176,387 bp (26.77%) number of C's = 13,947,871 bp (19.47%) number of T's = 21,942,590 bp (30.64%) number of G's = 16,446,963 bp (22.96%) number of N's = 107,101 bp (0.15%) GC percentage = 42.44% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 636,268 number of insertions = 5,258 mapped reads with insertion percentage = 0.48% number of deletions = 21,067 mapped reads with deletion percentage = 1.92% homopolymer indels = 44.07% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.3318X There is a 1.37% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% 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% 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 8232681 0.0330297311475906 0.6054185152022169 chr2 243199373 6514275 0.026785739287247257 0.4243528557031508 chr3 198022430 4111690 0.02076375893377331 0.22636884108994967 chr4 191154276 3328414 0.017412187002293373 0.20643073287591487 chr5 180915260 3692369 0.020409383929249528 0.21954169487931627 chr6 171115067 4141712 0.024204250815622216 0.26727094538716867 chr7 159138663 3333235 0.020945475707559513 0.47742385303686485 chr8 146364022 3749914 0.025620462930432453 0.32030017653285714 chr9 141213431 2709987 0.01919071706429964 0.2478531109725131 chr10 135534747 4788452 0.035330069269985796 0.4352716105605365 chr11 135006516 2608217 0.01931919345285527 0.22458147293178862 chr12 133851895 2800727 0.020924074328570394 0.2237727378524007 chr13 115169878 1478405 0.012836733229846783 0.17680587710138204 chr14 107349540 2051239 0.019108037165319943 0.21827449739773253 chr15 102531392 1929811 0.018821660004381877 0.2100301103272577 chr16 90354753 1286409 0.014237314112296893 0.21588082594056535 chr17 81195210 2248741 0.027695488440759006 0.26416674085274006 chr18 78077248 1352972 0.017328633304288594 0.31635005427377033 chr19 59128983 2686708 0.0454380891347311 0.4692254644084662 chr20 63025520 2208851 0.03504693019589525 0.29460388574043983 chr21 48129895 662304 0.013760761372947105 0.182646477442722 chr22 51304566 1826307 0.035597357942760886 0.29952487889884427 chrMT 16571 156147 9.422907488986784 7.0630861349817 chrX 155270560 3574101 0.023018536160364207 0.23680487536350825 chrY 59373566 184077 0.0031003190881275346 0.09444547741796123