BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716263.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 = 1,584,129 number of mapped reads = 1,257,927 (79.41%) number of supplementary alignments = 1,200 (0.08%) number of secondary alignments = 0 number of mapped bases = 65,440,250 bp number of sequenced bases = 65,422,567 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,703 duplication rate = 6.82% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8613 >>>>>>> ACTG content number of A's = 13,149,485 bp (20.1%) number of C's = 11,310,036 bp (17.29%) number of T's = 22,155,498 bp (33.87%) number of G's = 18,806,485 bp (28.75%) number of N's = 1,063 bp (0%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 419,555 number of insertions = 4,195 mapped reads with insertion percentage = 0.33% number of deletions = 10,410 mapped reads with deletion percentage = 0.82% homopolymer indels = 38.88% >>>>>>> Coverage mean coverageData = 0.0211X std coverageData = 0.1971X There is a 1.8% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 6794566 0.027259976214863674 0.24124286493446578 chr2 243199373 5128147 0.02108618511939996 0.2910959125675246 chr3 198022430 3630212 0.018332327302518204 0.1620578503772353 chr4 191154276 4293213 0.022459413882010153 0.18635141102378097 chr5 180915260 4184170 0.023127789220212823 0.17599531426594617 chr6 171115067 2987170 0.017457083425622594 0.1729318232644856 chr7 159138663 2212287 0.013901631183114816 0.15749629213315883 chr8 146364022 4273497 0.029197728660394422 0.20892185176797315 chr9 141213431 3060409 0.021672223232080522 0.18469780169614466 chr10 135534747 3538301 0.026106227947583067 0.2360044905101919 chr11 135006516 2950895 0.02185742649636259 0.19811946854280346 chr12 133851895 3314463 0.024762167169915673 0.1840800880316228 chr13 115169878 1205900 0.010470619757016674 0.12004365339403152 chr14 107349540 2237542 0.020843517354615586 0.16871060886115474 chr15 102531392 1372517 0.013386310019081766 0.13461069626577293 chr16 90354753 1830586 0.02025998565897247 0.17750526661291974 chr17 81195210 2766444 0.03407151727300169 0.2238425329871628 chr18 78077248 1833806 0.023487072700103365 0.21781467991751588 chr19 59128983 1904543 0.032209973914146296 0.24692703286261947 chr20 63025520 1870571 0.029679580588942385 0.20927952274042902 chr21 48129895 941459 0.019560794803312992 0.1724485161894323 chr22 51304566 779932 0.01520199975963153 0.14844631588031262 chrMT 16571 6068 0.36618188401424173 0.6957723975869948 chrX 155270560 2122179 0.013667619927435053 0.14473587382047673 chrY 59373566 201373 0.003391627176309403 0.10202123958985759