BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525206.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 = 3,339,911 number of mapped reads = 3,058,031 (91.56%) number of supplementary alignments = 9,476 (0.28%) number of secondary alignments = 0 number of mapped bases = 177,106,898 bp number of sequenced bases = 177,048,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,056 duplication rate = 3.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5346 >>>>>>> ACTG content number of A's = 43,673,169 bp (24.67%) number of C's = 35,408,929 bp (20%) number of T's = 57,263,762 bp (32.34%) number of G's = 40,698,769 bp (22.99%) number of N's = 4,270 bp (0%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 916,147 number of insertions = 11,365 mapped reads with insertion percentage = 0.37% number of deletions = 36,640 mapped reads with deletion percentage = 1.19% homopolymer indels = 43.26% >>>>>>> Coverage mean coverageData = 0.0572X std coverageData = 0.4907X There is a 4.88% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 18001734 0.07222342687764055 0.8854005007544155 chr2 243199373 13915943 0.057220307882948365 0.7066137709935533 chr3 198022430 12082456 0.06101559303155708 0.29028690915422617 chr4 191154276 9539286 0.04990359723891293 0.27637548859219035 chr5 180915260 7581673 0.04190731616559045 0.23555217814503193 chr6 171115067 10278969 0.06007050799331423 0.3380311328141195 chr7 159138663 12914141 0.0811502419119859 0.8544726889242216 chr8 146364022 11821505 0.08076783377816715 0.46843566193945396 chr9 141213431 5720896 0.04051240706700201 0.33727624509292015 chr10 135534747 9836018 0.07257192873204685 0.5170780105839705 chr11 135006516 7745082 0.0573682088055661 0.3865345585705568 chr12 133851895 7817942 0.05840740618576973 0.2823154605309428 chr13 115169878 5353930 0.046487242089463705 0.25528792741213274 chr14 107349540 6498416 0.06053510802188812 0.29700385616181524 chr15 102531392 4714946 0.045985389528311486 0.2655765710704267 chr16 90354753 5303092 0.05869189858778099 0.32834155254836334 chr17 81195210 3196255 0.03936506845662447 0.2433006381054826 chr18 78077248 3738228 0.04787858301563088 0.734105995110543 chr19 59128983 3361484 0.05685002226403928 0.6213720679833432 chr20 63025520 3176351 0.050397854710282436 0.2658163399942042 chr21 48129895 1857401 0.03859142015580961 0.24838122440369467 chr22 51304566 1935010 0.03771613622070207 0.22210474638741534 chrMT 16571 161520 9.747148633154305 5.735668334669889 chrX 155270560 10039294 0.064656777176562 0.3345742561343042 chrY 59373566 515326 0.008679384357678635 0.21069788406717926