BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716521.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 = 1,638,997 number of mapped reads = 1,536,733 (93.76%) number of supplementary alignments = 36,445 (2.22%) number of secondary alignments = 0 number of mapped bases = 118,709,436 bp number of sequenced bases = 118,660,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,648 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0547 >>>>>>> ACTG content number of A's = 29,200,407 bp (24.61%) number of C's = 25,320,163 bp (21.34%) number of T's = 35,713,743 bp (30.1%) number of G's = 28,420,884 bp (23.95%) number of N's = 5,030 bp (0%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 796,505 number of insertions = 11,288 mapped reads with insertion percentage = 0.72% number of deletions = 24,020 mapped reads with deletion percentage = 1.53% homopolymer indels = 38.93% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3277X There is a 3.24% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.08% 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 0.01% 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 13219998 0.05303897718272887 0.6160399244995522 chr2 243199373 11202863 0.04606452254299192 0.32771338794217214 chr3 198022430 7600764 0.03838334879538646 0.22573643582564953 chr4 191154276 5747967 0.03006977986723143 0.29542866938319834 chr5 180915260 7087244 0.03917438473680993 0.23249992916287804 chr6 171115067 7289044 0.042597324290560575 0.2520697529648204 chr7 159138663 7421337 0.046634405870306955 0.42607990665045187 chr8 146364022 7406866 0.05060578343494824 0.35383640045864123 chr9 141213431 3538844 0.025060250819909615 0.21806922514144625 chr10 135534747 6385946 0.047116670384163555 0.4592308798865937 chr11 135006516 3548213 0.02628179072482694 0.24599988636728262 chr12 133851895 4531169 0.03385210945276494 0.21215640690673473 chr13 115169878 2277831 0.01977801001056891 0.1585192578340928 chr14 107349540 2333778 0.02173999068836252 0.18230414097513714 chr15 102531392 2463562 0.024027392508237867 0.1764378656673487 chr16 90354753 3575198 0.039568455242194066 0.2438578833221856 chr17 81195210 2213412 0.027260376566548693 0.2123161505529445 chr18 78077248 3537534 0.04530812868814229 0.3563973526520631 chr19 59128983 3038412 0.05138617046736623 0.46341408770590786 chr20 63025520 2570388 0.04078328905497329 0.2461527802978666 chr21 48129895 2089007 0.043403522904008 0.2929938525573098 chr22 51304566 1911117 0.03725042718420033 0.22974652329476303 chrMT 16571 64380 3.885100476736467 3.0825846790005356 chrX 155270560 7225690 0.0465361237828987 0.26184211479551467 chrY 59373566 428872 0.007223281822082238 0.2638624308204531