BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231728.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,285,229 number of mapped reads = 4,931,253 (93.3%) number of supplementary alignments = 41,229 (0.78%) number of secondary alignments = 0 number of mapped bases = 337,328,176 bp number of sequenced bases = 337,200,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 554,072 duplication rate = 4.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8693 >>>>>>> ACTG content number of A's = 88,959,730 bp (26.38%) number of C's = 61,354,158 bp (18.2%) number of T's = 96,877,975 bp (28.73%) number of G's = 89,935,325 bp (26.67%) number of N's = 73,668 bp (0.02%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 2,172,340 number of insertions = 23,392 mapped reads with insertion percentage = 0.47% number of deletions = 77,727 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.43% >>>>>>> Coverage mean coverageData = 0.109X std coverageData = 39.0257X There is a 7.12% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 25272826 0.1013952378477725 1.3820900350017664 chr2 243199373 38754673 0.15935350705036563 139.2049708393545 chr3 198022430 36430987 0.1839740427384918 0.5834126935495114 chr4 191154276 15399339 0.08055974117994619 0.40846450946961516 chr5 180915260 28613843 0.15816157796749705 0.5453110454793302 chr6 171115067 26837062 0.15683634685424866 0.7674288472439255 chr7 159138663 26227569 0.1648095346886256 1.743602115050747 chr8 146364022 9667613 0.06605184025347431 0.8776239618100063 chr9 141213431 12949126 0.09169896877585249 0.786010221755873 chr10 135534747 6353669 0.04687852481105823 0.5551734578685121 chr11 135006516 11330507 0.0839256306710411 0.8038648821327452 chr12 133851895 3246033 0.024250930478048143 0.2523672669352581 chr13 115169878 13662682 0.11863068918072484 0.46558835476800126 chr14 107349540 10343922 0.0963573947312676 0.572472813792398 chr15 102531392 8764577 0.08548188831767738 0.39176853268051637 chr16 90354753 7301706 0.08081153185156735 0.4682406860294031 chr17 81195210 7351952 0.09054662214679905 0.5145204455048331 chr18 78077248 9641871 0.12349142992334976 1.63665691138954 chr19 59128983 8467040 0.14319610401552146 1.0202656907897627 chr20 63025520 8289808 0.13153097348502638 0.5267197285995705 chr21 48129895 7752832 0.1610814235102736 0.6072151568764971 chr22 51304566 3460095 0.06744224286002147 0.3473536025753927 chrMT 16571 12114 0.731036147486573 1.0893118105032815 chrX 155270560 10470578 0.06743440611021174 0.49300172680964754 chrY 59373566 725752 0.01222348679545372 0.23696439780249903