BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716825.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 = 1,643,367 number of mapped reads = 1,211,233 (73.7%) number of supplementary alignments = 1,430 (0.09%) number of secondary alignments = 0 number of mapped bases = 63,137,064 bp number of sequenced bases = 63,122,404 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,040 duplication rate = 8.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9999 >>>>>>> ACTG content number of A's = 13,973,475 bp (22.14%) number of C's = 10,846,810 bp (17.18%) number of T's = 20,214,281 bp (32.02%) number of G's = 18,086,680 bp (28.65%) number of N's = 1,158 bp (0%) GC percentage = 45.84% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 416,020 number of insertions = 3,747 mapped reads with insertion percentage = 0.31% number of deletions = 8,618 mapped reads with deletion percentage = 0.71% homopolymer indels = 40.71% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 0.1964X There is a 1.67% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.06% 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 6407500 0.025707057315616476 0.21090439382436243 chr2 243199373 5457549 0.022440637624505717 0.31906792938990647 chr3 198022430 4306858 0.02174934425357774 0.17972408097450976 chr4 191154276 4096559 0.02143064275475585 0.1795848570021691 chr5 180915260 3586453 0.01982393856659742 0.17065526183444604 chr6 171115067 2835770 0.016572298686006418 0.18722671497387147 chr7 159138663 3447170 0.021661423660446363 0.18974103093043512 chr8 146364022 3710432 0.025350710846139497 0.198903831179059 chr9 141213431 2865004 0.020288466753562558 0.18314160316386388 chr10 135534747 3192613 0.023555679046643293 0.2003519747587153 chr11 135006516 2950282 0.02185288597477769 0.19537815377358056 chr12 133851895 3006393 0.02246059347908373 0.18315742382313743 chr13 115169878 946195 0.008215646455751216 0.11192445077395555 chr14 107349540 2098682 0.019549985961747018 0.1704415281301795 chr15 102531392 1240205 0.012095856457308216 0.13468684182881646 chr16 90354753 1782500 0.019727794507943593 0.17553679044501402 chr17 81195210 2530040 0.031159966209829373 0.22151407034136522 chr18 78077248 1659664 0.021256691834220385 0.19957938982994436 chr19 59128983 1589103 0.02687519587475401 0.23927738609232474 chr20 63025520 1641731 0.026048670443337873 0.2038496070603728 chr21 48129895 834820 0.017345144841890887 0.16270438016942956 chr22 51304566 659645 0.012857432611358606 0.14094845690631488 chrMT 16571 3881 0.23420433287067768 0.5770568151120756 chrX 155270560 2119378 0.013649580448476518 0.14585187305890154 chrY 59373566 168637 0.002840270702285256 0.07686038507348934