BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524606.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,348,734 number of mapped reads = 1,250,928 (92.75%) number of supplementary alignments = 2,903 (0.22%) number of secondary alignments = 0 number of mapped bases = 72,629,911 bp number of sequenced bases = 72,606,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,791 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2937 >>>>>>> ACTG content number of A's = 18,458,616 bp (25.42%) number of C's = 14,012,822 bp (19.3%) number of T's = 22,870,686 bp (31.5%) number of G's = 17,264,176 bp (23.78%) number of N's = 439 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 343,392 number of insertions = 3,872 mapped reads with insertion percentage = 0.31% number of deletions = 13,629 mapped reads with deletion percentage = 1.08% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.2223X There is a 2.09% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 7598795 0.03048656396326491 0.3556778916954507 chr2 243199373 6558774 0.02696871262081749 0.26183411828249326 chr3 198022430 4201874 0.021219182089624897 0.16168737320101578 chr4 191154276 3383762 0.017701733232480765 0.16446506389150556 chr5 180915260 4540199 0.02509572161021685 0.17480013583936738 chr6 171115067 4838891 0.02827857934918145 0.1956711196033417 chr7 159138663 4548336 0.028580961497709705 0.3070858646421913 chr8 146364022 6652506 0.04545178459225451 0.3049037079890676 chr9 141213431 2690938 0.019055821963563792 0.201338773127454 chr10 135534747 3181219 0.023471612043515305 0.22284909545161244 chr11 135006516 3647918 0.02702031063448819 0.21400113421372038 chr12 133851895 2205884 0.016480035639390836 0.1468753998409312 chr13 115169878 1489165 0.01293016043656832 0.12497787854939578 chr14 107349540 1378633 0.012842467699442401 0.13046489740117828 chr15 102531392 1862500 0.01816516838082136 0.15442190069615314 chr16 90354753 1826171 0.020211122706516614 0.1639391929798307 chr17 81195210 1618176 0.019929451503358387 0.1596418958666546 chr18 78077248 1962896 0.025140435277636836 0.30801902991865054 chr19 59128983 1480866 0.025044672254890633 0.2596943750185929 chr20 63025520 1402125 0.022246940604377402 0.1677430416137959 chr21 48129895 658048 0.013672334003637448 0.14144898136751294 chr22 51304566 1334358 0.026008562278842785 0.1779778358577841 chrMT 16571 14123 0.8522720415183151 1.0772405626634654 chrX 155270560 3372448 0.02171981604239722 0.18153810781098811 chrY 59373566 181306 0.0030536484872746234 0.09524226940114208