BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672002.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 16,748,204 number of mapped reads = 16,403,901 (97.94%) number of supplementary alignments = 140,115 (0.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,203,380 number of mapped paired reads (second in pair) = 8,200,521 number of mapped paired reads (both in pair) = 16,383,072 number of mapped paired reads (singletons) = 20,829 number of mapped bases = 2,231,621,744 bp number of sequenced bases = 2,230,902,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,698,987 duplication rate = 58.75% >>>>>>> Insert size mean insert size = 41,469.1788 std insert size = 1,990,304.8482 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 52.5401 >>>>>>> ACTG content number of A's = 569,260,061 bp (25.52%) number of C's = 505,500,199 bp (22.66%) number of T's = 598,931,468 bp (26.85%) number of G's = 557,204,691 bp (24.98%) number of N's = 5,871 bp (0%) GC percentage = 47.64% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 16,762,416 number of insertions = 165,856 mapped reads with insertion percentage = 0.97% number of deletions = 417,100 mapped reads with deletion percentage = 2.5% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 0.7209X std coverageData = 40.9867X There is a 3.25% of reference with a coverageData >= 1X There is a 1.67% of reference with a coverageData >= 2X There is a 0.6% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.25% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.14% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.13% of reference with a coverageData >= 19X There is a 0.13% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.12% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.12% of reference with a coverageData >= 24X There is a 0.12% of reference with a coverageData >= 25X There is a 0.12% of reference with a coverageData >= 26X There is a 0.12% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.11% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.11% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.11% of reference with a coverageData >= 35X There is a 0.11% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.1% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 273339262 1.0966442567057837 52.71329458363829 chr2 243199373 223327357 0.9182891972340734 48.95133310505279 chr3 198022430 15723618 0.07940321710020426 5.829813661454069 chr4 191154276 136530018 0.7142399367514017 40.24558193238924 chr5 180915260 84282658 0.46586815285786287 32.493683130095114 chr6 171115067 141138495 0.8248162916010195 42.20486908872912 chr7 159138663 130891372 0.8224988794834854 47.661055231912 chr8 146364022 10573737 0.07224273325858728 4.757976568943627 chr9 141213431 98678348 0.6987886867503418 41.73684560820218 chr10 135534747 100286015 0.7399284480163599 42.030260495129596 chr11 135006516 170360249 1.2618668642630553 55.80177177616128 chr12 133851895 109565879 0.818560536628936 44.2851711356186 chr13 115169878 75122441 0.6522750766480798 38.62579230679343 chr14 107349540 62603629 0.5831755683349924 32.93757315561941 chr15 102531392 86858899 0.8471444433330233 40.718041629735445 chr16 90354753 83784931 0.9272885843647871 39.295804862390106 chr17 81195210 140535480 1.730834614504969 62.001897889034254 chr18 78077248 6292393 0.0805918902264588 4.00200720979872 chr19 59128983 28256961 0.47788680891061497 30.14006930639946 chr20 63025520 35989821 0.5710356852271905 33.481737554319665 chr21 48129895 37107453 0.7709855381982446 70.54573250829772 chr22 51304566 3409710 0.0664601665278681 4.1817417958823935 chrMT 16571 88028 5.312171866513789 9.687223134882577 chrX 155270560 170800620 1.100019346874256 43.984087734974544 chrY 59373566 6074370 0.10230764983865041 7.144963607611624