BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717054.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 = 933,610 number of mapped reads = 756,438 (81.02%) number of supplementary alignments = 3,177 (0.34%) number of secondary alignments = 0 number of mapped bases = 42,481,594 bp number of sequenced bases = 42,469,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,680 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5555 >>>>>>> ACTG content number of A's = 10,351,127 bp (24.37%) number of C's = 8,641,518 bp (20.35%) number of T's = 12,264,908 bp (28.88%) number of G's = 11,210,317 bp (26.4%) number of N's = 1,286 bp (0%) GC percentage = 46.74% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 224,409 number of insertions = 3,358 mapped reads with insertion percentage = 0.44% number of deletions = 7,272 mapped reads with deletion percentage = 0.95% homopolymer indels = 34.48% >>>>>>> Coverage mean coverageData = 0.0137X std coverageData = 0.1411X There is a 1.27% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 3999354 0.016045512680989468 0.16875973163147115 chr2 243199373 3512997 0.014444926221088571 0.16206208072315764 chr3 198022430 2772606 0.014001474479431446 0.12835985321265525 chr4 191154276 2614772 0.013678856966819827 0.14090669074746495 chr5 180915260 3548179 0.019612380956697626 0.14970243514773188 chr6 171115067 1812141 0.010590189582779406 0.11093452861782041 chr7 159138663 2320789 0.014583439098014793 0.1525177467546554 chr8 146364022 2491866 0.017025126571064027 0.1431356746240969 chr9 141213431 1793553 0.012701008588906815 0.12855177978848276 chr10 135534747 2161930 0.01595111252172109 0.1964940098177739 chr11 135006516 1692058 0.012533158029202086 0.13726019942227424 chr12 133851895 1968151 0.014703945730465752 0.12978450536901184 chr13 115169878 712914 0.0061901081461595365 0.08531755544896326 chr14 107349540 1804268 0.016807412495666026 0.13921613693095125 chr15 102531392 815267 0.007951389170645416 0.09621077571030888 chr16 90354753 1121847 0.0124160264153453 0.12673256437268376 chr17 81195210 1630633 0.020082871883698557 0.15839590656654173 chr18 78077248 1098775 0.01407292173002819 0.166506427377739 chr19 59128983 1083335 0.01832155645227316 0.16039640177735653 chr20 63025520 1038954 0.016484655739452844 0.14624597140411583 chr21 48129895 565814 0.011755978275040907 0.12774557741214937 chr22 51304566 454683 0.008862427566388536 0.10238506169784246 chrMT 16571 11133 0.6718363405950154 0.942361267499843 chrX 155270560 1313218 0.008457611024266287 0.10221863521419806 chrY 59373566 142357 0.002397649485968217 0.08659866466384292