BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237594.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 = 1,256,842 number of mapped reads = 942,636 (75%) number of supplementary alignments = 4,183 (0.33%) number of secondary alignments = 0 number of mapped bases = 58,224,494 bp number of sequenced bases = 58,186,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,324 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7879 >>>>>>> ACTG content number of A's = 15,400,323 bp (26.47%) number of C's = 10,031,821 bp (17.24%) number of T's = 18,499,776 bp (31.79%) number of G's = 14,152,676 bp (24.32%) number of N's = 101,724 bp (0.17%) GC percentage = 41.56% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 587,683 number of insertions = 5,732 mapped reads with insertion percentage = 0.6% number of deletions = 22,964 mapped reads with deletion percentage = 2.4% homopolymer indels = 48.16% >>>>>>> Coverage mean coverageData = 0.0188X std coverageData = 0.2251X There is a 1.58% of reference with a coverageData >= 1X There is a 0.18% 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 5083447 0.020394922105329477 0.26202605907709536 chr2 243199373 5118793 0.021047722849186785 0.3526462830793934 chr3 198022430 4102342 0.020716552160278005 0.1765017275349959 chr4 191154276 3718173 0.019451163101368445 0.17273280968080276 chr5 180915260 3217753 0.017785967861417548 0.1576291244889839 chr6 171115067 3034926 0.01773617047994961 0.19310906877985742 chr7 159138663 3459298 0.021737633927463623 0.30335696127286327 chr8 146364022 3163771 0.02161576975522031 0.22098669341149232 chr9 141213431 2418694 0.017127931690860198 0.2301254007252254 chr10 135534747 2437818 0.0179866643348661 0.20080749703481982 chr11 135006516 2397012 0.01775478748003541 0.21495963939048243 chr12 133851895 3494028 0.02610368721339358 0.2034673746466222 chr13 115169878 2047898 0.01778154180210211 0.1698339939193767 chr14 107349540 1598316 0.01488889472651676 0.16255769166432993 chr15 102531392 1832445 0.017872038643540505 0.1642277245078538 chr16 90354753 1474090 0.016314471027329355 0.16595678474586065 chr17 81195210 1358788 0.016734829554600573 0.16635152797900096 chr18 78077248 1544161 0.019777349222144715 0.43063492807172765 chr19 59128983 1000632 0.016922868434926405 0.20661835111915358 chr20 63025520 1162784 0.01844941541140795 0.16605628428987343 chr21 48129895 690906 0.014355028200248515 0.15877937280968787 chr22 51304566 578470 0.011275214763535862 0.127055366839686 chrMT 16571 39461 2.381328827469676 2.2460960304923345 chrX 155270560 3043852 0.01960353591820626 0.1809157445924175 chrY 59373566 206636 0.003480269317157066 0.09129885586844683