BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716095.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 = 935,465 number of mapped reads = 838,604 (89.65%) number of supplementary alignments = 4,547 (0.49%) number of secondary alignments = 0 number of mapped bases = 48,916,452 bp number of sequenced bases = 48,901,769 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,638 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8277 >>>>>>> ACTG content number of A's = 12,636,613 bp (25.84%) number of C's = 9,805,502 bp (20.05%) number of T's = 14,993,028 bp (30.66%) number of G's = 11,466,310 bp (23.45%) number of N's = 316 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 247,069 number of insertions = 3,797 mapped reads with insertion percentage = 0.45% number of deletions = 9,046 mapped reads with deletion percentage = 1.07% homopolymer indels = 40.77% >>>>>>> Coverage mean coverageData = 0.0158X std coverageData = 0.1687X There is a 1.45% 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% 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 5980761 0.023994969304409475 0.24730347150347295 chr2 243199373 5012967 0.02061258192470751 0.23055422786308108 chr3 198022430 3054499 0.015425015236910283 0.13235479693276345 chr4 191154276 2034800 0.010644805036953503 0.1254660472055282 chr5 180915260 3484892 0.019262565247398146 0.1484645287297502 chr6 171115067 1792575 0.01047584547303482 0.11471254999757916 chr7 159138663 3271866 0.020559843461799097 0.2427755865547899 chr8 146364022 2155447 0.014726617720302876 0.15745964677036559 chr9 141213431 1338255 0.009476825189524642 0.1301382872503894 chr10 135534747 2178764 0.016075316833697267 0.1607813976027079 chr11 135006516 2073016 0.015354932942644043 0.16688554251444188 chr12 133851895 1946965 0.014545666312755601 0.12974621589329824 chr13 115169878 1380360 0.011985425564139262 0.11632854151958387 chr14 107349540 1036468 0.009655076304938056 0.10830254624531838 chr15 102531392 2106411 0.020544059325752644 0.15423564756970037 chr16 90354753 1427875 0.015802987143354815 0.14082289091231862 chr17 81195210 1856072 0.02285937803473875 0.16939201520436223 chr18 78077248 1537379 0.01969048652944325 0.25851711035681013 chr19 59128983 767789 0.012984985721807528 0.1794074228659563 chr20 63025520 1291416 0.020490366442038083 0.15455476245401428 chr21 48129895 626768 0.013022426082583392 0.1279812366386022 chr22 51304566 626150 0.012204566743630577 0.11720032245552095 chrMT 16571 8199 0.49478003741476073 0.7541360055070481 chrX 155270560 1796506 0.011570165007455373 0.12277659306942187 chrY 59373566 130252 0.002193770877767389 0.07386717813580064