BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716512.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 = 833,424 number of mapped reads = 770,765 (92.48%) number of supplementary alignments = 4,247 (0.51%) number of secondary alignments = 0 number of mapped bases = 45,764,032 bp number of sequenced bases = 45,750,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,202 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8357 >>>>>>> ACTG content number of A's = 11,962,091 bp (26.15%) number of C's = 9,299,559 bp (20.33%) number of T's = 13,933,290 bp (30.45%) number of G's = 10,555,134 bp (23.07%) number of N's = 619 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 222,563 number of insertions = 3,811 mapped reads with insertion percentage = 0.49% number of deletions = 8,488 mapped reads with deletion percentage = 1.09% homopolymer indels = 40.25% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1633X There is a 1.38% 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 3774328 0.015142702493006026 0.23682986786936322 chr2 243199373 4438477 0.018250363663560927 0.19098452997676368 chr3 198022430 3370402 0.01702030421503261 0.14013877100892402 chr4 191154276 2779038 0.014538194269847251 0.13411294980198243 chr5 180915260 2416427 0.013356678701398655 0.12027039414788371 chr6 171115067 2543842 0.014866265400229192 0.1320921119568492 chr7 159138663 2411212 0.015151641684962504 0.24661734183744188 chr8 146364022 3758934 0.025682090097250813 0.20250897364366355 chr9 141213431 1895824 0.01342523856671962 0.1303367264533528 chr10 135534747 2172770 0.016031092012146524 0.21650067510605137 chr11 135006516 1574643 0.011663459265921654 0.12569825685166278 chr12 133851895 2117006 0.015816033086419882 0.13999535838940935 chr13 115169878 1178574 0.01023335285637795 0.10507783322985367 chr14 107349540 1114946 0.010386127411444892 0.10689979025421097 chr15 102531392 1088726 0.010618465025813753 0.10865278059275982 chr16 90354753 1379154 0.015263768138461958 0.13260986556990795 chr17 81195210 1898135 0.023377425835834405 0.1636501690561205 chr18 78077248 1060163 0.013578385857042503 0.18344411722426418 chr19 59128983 920148 0.01556170854486031 0.21144546063198288 chr20 63025520 1018700 0.016163293853029694 0.13930656667394886 chr21 48129895 470987 0.00978574750682502 0.10812786852353738 chr22 51304566 694587 0.013538502596435568 0.12152664685212507 chrMT 16571 8555 0.5162633516384044 0.7882566602014264 chrX 155270560 1574191 0.010138373945453664 0.11374340492011818 chrY 59373566 104263 0.0017560508324529472 0.056303932736807526