BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716544.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 = 723,696 number of mapped reads = 630,561 (87.13%) number of supplementary alignments = 2,763 (0.38%) number of secondary alignments = 0 number of mapped bases = 36,520,160 bp number of sequenced bases = 36,509,333 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,037 duplication rate = 2.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1597 >>>>>>> ACTG content number of A's = 9,281,978 bp (25.42%) number of C's = 7,127,596 bp (19.52%) number of T's = 11,476,926 bp (31.44%) number of G's = 8,621,765 bp (23.62%) number of N's = 1,068 bp (0%) GC percentage = 43.14% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 184,116 number of insertions = 2,419 mapped reads with insertion percentage = 0.38% number of deletions = 6,922 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.84% >>>>>>> Coverage mean coverageData = 0.0118X std coverageData = 0.1412X There is a 1.1% of reference with a coverageData >= 1X There is a 0.06% 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 2967816 0.011906955288990032 0.22793060076379437 chr2 243199373 3104677 0.012765974524120175 0.18065848963778977 chr3 198022430 2407416 0.012157289454533005 0.1160561492938064 chr4 191154276 2276566 0.011909574023863322 0.11854408619728467 chr5 180915260 2199079 0.012155298563537427 0.11656977743372146 chr6 171115067 2150839 0.012569547718436741 0.12857718703034857 chr7 159138663 2004997 0.01259905645933446 0.15738093979213333 chr8 146364022 1831857 0.012515760191394576 0.13511936047797643 chr9 141213431 1522021 0.010778160329522763 0.12185062610389717 chr10 135534747 1780576 0.013137413389645388 0.13928485808976648 chr11 135006516 1673441 0.012395260981329228 0.13007008085158567 chr12 133851895 1647616 0.012309246723776306 0.11785046910470139 chr13 115169878 1144507 0.00993755502632381 0.10483233712891202 chr14 107349540 1084635 0.010103769424629113 0.10651935132208135 chr15 102531392 1054567 0.010285308522876584 0.10641637035082194 chr16 90354753 1059317 0.011723976490755279 0.11662086301761149 chr17 81195210 1001307 0.012332094467148986 0.118910838377667 chr18 78077248 950599 0.012175108938265856 0.1779170706416403 chr19 59128983 769989 0.01302219251766938 0.16414858654103398 chr20 63025520 781901 0.012406101528396751 0.11747758411060616 chr21 48129895 481480 0.010003761695303927 0.10935985142528468 chr22 51304566 448270 0.008737428945408094 0.09823047176955486 chrMT 16571 7771 0.46895178323577336 0.7365002738675807 chrX 155270560 2055703 0.013239489829881466 0.12620428279620896 chrY 59373566 113213 0.0019067913151788794 0.06171566005960601