BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671994.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 = 600,251,144 number of mapped reads = 592,406,711 (98.69%) number of supplementary alignments = 10,441,937 (1.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 296,704,971 number of mapped paired reads (second in pair) = 295,701,740 number of mapped paired reads (both in pair) = 588,652,946 number of mapped paired reads (singletons) = 3,753,765 number of mapped bases = 80,148,924,056 bp number of sequenced bases = 80,102,385,739 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 327,404,697 duplication rate = 38.61% >>>>>>> Insert size mean insert size = 201,788.39 std insert size = 4,566,053.6925 median insert size = 319 >>>>>>> Mapping quality mean mapping quality = 53.7388 >>>>>>> ACTG content number of A's = 20,439,765,576 bp (25.52%) number of C's = 16,949,121,147 bp (21.16%) number of T's = 22,046,736,137 bp (27.52%) number of G's = 20,666,541,054 bp (25.8%) number of N's = 221,825 bp (0%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 895,456,892 number of insertions = 12,576,993 mapped reads with insertion percentage = 2.02% number of deletions = 23,910,539 mapped reads with deletion percentage = 3.91% homopolymer indels = 46.23% >>>>>>> Coverage mean coverageData = 25.8905X std coverageData = 186.6837X There is a 66.64% of reference with a coverageData >= 1X There is a 60.22% of reference with a coverageData >= 2X There is a 55.68% of reference with a coverageData >= 3X There is a 52.21% of reference with a coverageData >= 4X There is a 49.33% of reference with a coverageData >= 5X There is a 46.88% of reference with a coverageData >= 6X There is a 44.73% of reference with a coverageData >= 7X There is a 42.81% of reference with a coverageData >= 8X There is a 41.08% of reference with a coverageData >= 9X There is a 39.5% of reference with a coverageData >= 10X There is a 38.06% of reference with a coverageData >= 11X There is a 36.72% of reference with a coverageData >= 12X There is a 35.49% of reference with a coverageData >= 13X There is a 34.33% of reference with a coverageData >= 14X There is a 33.25% of reference with a coverageData >= 15X There is a 32.23% of reference with a coverageData >= 16X There is a 31.27% of reference with a coverageData >= 17X There is a 30.36% of reference with a coverageData >= 18X There is a 29.51% of reference with a coverageData >= 19X There is a 28.69% of reference with a coverageData >= 20X There is a 27.92% of reference with a coverageData >= 21X There is a 27.18% of reference with a coverageData >= 22X There is a 26.47% of reference with a coverageData >= 23X There is a 25.8% of reference with a coverageData >= 24X There is a 25.16% of reference with a coverageData >= 25X There is a 24.54% of reference with a coverageData >= 26X There is a 23.95% of reference with a coverageData >= 27X There is a 23.38% of reference with a coverageData >= 28X There is a 22.83% of reference with a coverageData >= 29X There is a 22.31% of reference with a coverageData >= 30X There is a 21.8% of reference with a coverageData >= 31X There is a 21.31% of reference with a coverageData >= 32X There is a 20.84% of reference with a coverageData >= 33X There is a 20.39% of reference with a coverageData >= 34X There is a 19.95% of reference with a coverageData >= 35X There is a 19.52% of reference with a coverageData >= 36X There is a 19.11% of reference with a coverageData >= 37X There is a 18.71% of reference with a coverageData >= 38X There is a 18.33% of reference with a coverageData >= 39X There is a 17.96% of reference with a coverageData >= 40X There is a 17.59% of reference with a coverageData >= 41X There is a 17.24% of reference with a coverageData >= 42X There is a 16.9% of reference with a coverageData >= 43X There is a 16.57% of reference with a coverageData >= 44X There is a 16.25% of reference with a coverageData >= 45X There is a 15.94% of reference with a coverageData >= 46X There is a 15.63% of reference with a coverageData >= 47X There is a 15.34% of reference with a coverageData >= 48X There is a 15.05% of reference with a coverageData >= 49X There is a 14.77% of reference with a coverageData >= 50X There is a 14.5% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6975479261 27.985804942086784 170.5516732699943 chr2 243199373 6651489848 27.349946531317745 433.71379655905724 chr3 198022430 4790969295 24.194073848098924 54.29069187340804 chr4 191154276 4104752361 21.473505311489866 103.97944160313341 chr5 180915260 4403269697 24.338851775134945 55.76831529023082 chr6 171115067 4153402378 24.272569627080237 184.70507684653109 chr7 159138663 3980848931 25.014970315541735 97.16031369851285 chr8 146364022 3652079788 24.952032187254325 67.20293994859084 chr9 141213431 3534979462 25.03288417374407 254.84206249809307 chr10 135534747 3821984295 28.19929486421663 65.36663848569084 chr11 135006516 3996060507 29.599019553989528 221.14359006511987 chr12 133851895 3559284919 26.591217995083298 62.01586318888298 chr13 115169878 1978970865 17.183059488870867 44.856555097175175 chr14 107349540 2399172310 22.349162464971904 106.31078403825282 chr15 102531392 2461318978 24.00551606672813 56.56086701937454 chr16 90354753 2998397504 33.18472359721906 194.7073824499358 chr17 81195210 3154190429 38.84700130709681 269.6543882119394 chr18 78077248 1965432856 25.17292689414463 357.84307055539233 chr19 59128983 2386426164 40.35966869242449 89.60364334015533 chr20 63025520 2230893535 35.39667003144123 79.82600190622694 chr21 48129895 1110815513 23.079533271369073 214.85563053237163 chr22 51304566 1580158677 30.79957204978598 67.93827864154194 chrMT 16571 66093 3.9884738398406854 12.129274646242234 chrX 155270560 4092291213 26.35587334134687 104.03106772414999 chrY 59373566 166189177 2.7990432139447377 100.72370479498744