BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716761.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 = 1,155,183 number of mapped reads = 979,132 (84.76%) number of supplementary alignments = 2,786 (0.24%) number of secondary alignments = 0 number of mapped bases = 54,785,569 bp number of sequenced bases = 54,770,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,495 duplication rate = 1.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.8217 >>>>>>> ACTG content number of A's = 13,167,093 bp (24.04%) number of C's = 11,429,827 bp (20.87%) number of T's = 16,501,150 bp (30.13%) number of G's = 13,671,293 bp (24.96%) number of N's = 1,443 bp (0%) GC percentage = 45.83% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 288,632 number of insertions = 4,262 mapped reads with insertion percentage = 0.43% number of deletions = 9,097 mapped reads with deletion percentage = 0.92% homopolymer indels = 37.73% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.1655X There is a 1.63% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 5277837 0.02117481986133146 0.19902978880327807 chr2 243199373 4657899 0.019152594608046133 0.20365409862544134 chr3 198022430 3588407 0.01812121485429706 0.14552347800616278 chr4 191154276 3520661 0.018417903453020325 0.16822523107616552 chr5 180915260 3268182 0.018064711622446886 0.14415494752957062 chr6 171115067 2355930 0.013768103775455379 0.1279928260165639 chr7 159138663 3125652 0.019641059822150198 0.18581541998068338 chr8 146364022 3317532 0.02266630798106928 0.170335339213562 chr9 141213431 2360389 0.016715046035529015 0.15225172539929974 chr10 135534747 2784865 0.020547240184836144 0.23946254210526563 chr11 135006516 2239773 0.016590110361784316 0.16010358307139302 chr12 133851895 2631981 0.019663382427271576 0.15091875550691425 chr13 115169878 945056 0.008205756717047144 0.09604334360321681 chr14 107349540 2480675 0.023108389658679486 0.16568531309208911 chr15 102531392 1066288 0.010399624731516373 0.11190076792873396 chr16 90354753 1483834 0.016422312614810645 0.14688187705378505 chr17 81195210 2164480 0.0266577301789108 0.18273658317174224 chr18 78077248 1404771 0.01799206601134302 0.1880422619175157 chr19 59128983 1460654 0.024702843273999825 0.19245883174890915 chr20 63025520 1409119 0.02235791152536306 0.16506349987393673 chr21 48129895 749802 0.015578716720657712 0.14932042022627398 chr22 51304566 592672 0.011552032230425651 0.11603018702195073 chrMT 16571 17121 1.0331905135477641 1.3752705688795022 chrX 155270560 1705271 0.010982577766190835 0.12124897244261282 chrY 59373566 176718 0.002976375042051542 0.09906514897065213