BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867834.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 = 1,558,153 number of mapped reads = 1,437,576 (92.26%) number of supplementary alignments = 6,215 (0.4%) number of secondary alignments = 0 number of mapped bases = 85,227,572 bp number of sequenced bases = 85,201,688 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,103 duplication rate = 2.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.018 >>>>>>> ACTG content number of A's = 21,614,450 bp (25.37%) number of C's = 14,600,530 bp (17.14%) number of T's = 27,183,712 bp (31.91%) number of G's = 21,791,520 bp (25.58%) number of N's = 11,476 bp (0.01%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 422,071 number of insertions = 6,125 mapped reads with insertion percentage = 0.42% number of deletions = 16,179 mapped reads with deletion percentage = 1.12% homopolymer indels = 44.01% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2721X There is a 2.5% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% 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 7109915 0.02852516463740325 0.5103750590571724 chr2 243199373 7115944 0.029259713593093845 0.3412070177008517 chr3 198022430 5858566 0.029585365657819673 0.18616700172543066 chr4 191154276 5622878 0.02941539220393898 0.20951651540833147 chr5 180915260 5049927 0.02791321749199045 0.18174663439839764 chr6 171115067 4677412 0.02733489272455476 0.19947918358838945 chr7 159138663 4562130 0.028667640622316904 0.3014005037545244 chr8 146364022 4177615 0.028542635976483346 0.29150062013682104 chr9 141213431 3699819 0.026200191963326774 0.22925456857624935 chr10 135534747 4232049 0.031224826796629503 0.28675346624425146 chr11 135006516 3858645 0.028581176037458814 0.2304578373389865 chr12 133851895 3675843 0.027462016880672478 0.1813551116851993 chr13 115169878 2680545 0.023274705561466342 0.16529664003364455 chr14 107349540 2542713 0.023686296187203037 0.1702656545455694 chr15 102531392 2537412 0.024747659721619696 0.17001089201863304 chr16 90354753 2464432 0.027275067643646816 0.1923416615287223 chr17 81195210 2291483 0.028221898804128964 0.1947552292828865 chr18 78077248 2272015 0.02909957840727173 0.4039830932814096 chr19 59128983 1768231 0.029904640842545863 0.3728833362681512 chr20 63025520 1743842 0.027668823676504375 0.1853498425216596 chr21 48129895 1125171 0.023377798767273437 0.18786709044845235 chr22 51304566 1014914 0.01978213790951862 0.15160888242649476 chrMT 16571 26752 1.614386578963249 1.6129842867858157 chrX 155270560 4824906 0.031074184314141714 0.20774113232833674 chrY 59373566 294413 0.004958654496177642 0.20242386345773303