BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672000.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 = 309,374,548 number of mapped reads = 307,917,902 (99.53%) number of supplementary alignments = 1,404,584 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 154,007,893 number of mapped paired reads (second in pair) = 153,910,009 number of mapped paired reads (both in pair) = 307,377,032 number of mapped paired reads (singletons) = 540,870 number of mapped bases = 45,642,185,705 bp number of sequenced bases = 45,623,967,533 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,364,861 duplication rate = 26.47% >>>>>>> Insert size mean insert size = 60,183.3498 std insert size = 2,354,244.1017 median insert size = 331 >>>>>>> Mapping quality mean mapping quality = 54.5649 >>>>>>> ACTG content number of A's = 13,360,190,265 bp (29.28%) number of C's = 9,485,477,586 bp (20.79%) number of T's = 13,285,787,116 bp (29.12%) number of G's = 9,492,286,592 bp (20.81%) number of N's = 225,974 bp (0%) GC percentage = 41.6% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 298,497,082 number of insertions = 6,131,167 mapped reads with insertion percentage = 1.89% number of deletions = 6,642,993 mapped reads with deletion percentage = 2.07% homopolymer indels = 45.65% >>>>>>> Coverage mean coverageData = 14.7438X std coverageData = 143.2335X There is a 92.21% of reference with a coverageData >= 1X There is a 92% of reference with a coverageData >= 2X There is a 91.63% of reference with a coverageData >= 3X There is a 91.01% of reference with a coverageData >= 4X There is a 90.06% of reference with a coverageData >= 5X There is a 88.68% of reference with a coverageData >= 6X There is a 86.77% of reference with a coverageData >= 7X There is a 84.23% of reference with a coverageData >= 8X There is a 80.99% of reference with a coverageData >= 9X There is a 76.99% of reference with a coverageData >= 10X There is a 72.24% of reference with a coverageData >= 11X There is a 66.82% of reference with a coverageData >= 12X There is a 60.85% of reference with a coverageData >= 13X There is a 54.52% of reference with a coverageData >= 14X There is a 48.04% of reference with a coverageData >= 15X There is a 41.63% of reference with a coverageData >= 16X There is a 35.47% of reference with a coverageData >= 17X There is a 29.73% of reference with a coverageData >= 18X There is a 24.53% of reference with a coverageData >= 19X There is a 19.93% of reference with a coverageData >= 20X There is a 15.97% of reference with a coverageData >= 21X There is a 12.63% of reference with a coverageData >= 22X There is a 9.87% of reference with a coverageData >= 23X There is a 7.64% of reference with a coverageData >= 24X There is a 5.86% of reference with a coverageData >= 25X There is a 4.48% of reference with a coverageData >= 26X There is a 3.41% of reference with a coverageData >= 27X There is a 2.6% of reference with a coverageData >= 28X There is a 1.99% of reference with a coverageData >= 29X There is a 1.54% of reference with a coverageData >= 30X There is a 1.2% of reference with a coverageData >= 31X There is a 0.96% of reference with a coverageData >= 32X There is a 0.78% of reference with a coverageData >= 33X There is a 0.65% of reference with a coverageData >= 34X There is a 0.56% of reference with a coverageData >= 35X There is a 0.49% of reference with a coverageData >= 36X There is a 0.43% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.34% of reference with a coverageData >= 40X There is a 0.31% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.24% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.21% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3752931120 15.056857651720755 300.87069659174665 chr2 243199373 3921464748 16.124485436070593 89.49483404959311 chr3 198022430 3021137947 15.256544155124246 10.226981626557471 chr4 191154276 2990262807 15.643190775392332 98.22966390949763 chr5 180915260 2759289991 15.25183663887723 12.460815518633378 chr6 171115067 2637880641 15.415829168333843 71.46160858684419 chr7 159138663 2494172424 15.672950727253502 120.76066970085186 chr8 146364022 2289209280 15.64051908876896 95.185803031829 chr9 141213431 2003497016 14.187722809454293 223.1332643790727 chr10 135534747 2425569364 17.89629167197988 347.5857379147413 chr11 135006516 2114566592 15.662700250704937 62.26098462308273 chr12 133851895 2033966121 15.195646807988785 11.142947002052498 chr13 115169878 1456363916 12.64535433475062 8.642319211939117 chr14 107349540 1396482800 13.008745077063208 10.638204386012225 chr15 102531392 1317469257 12.849423296623145 8.96337744054947 chr16 90354753 1473461057 16.307510209230497 99.86281748025718 chr17 81195210 1330463670 16.385987178307687 77.42179272635997 chr18 78077248 1312259217 16.807190962980663 227.88755707819433 chr19 59128983 953755277 16.130080860683837 133.76320794434935 chr20 63025520 987599501 15.66983502873122 36.492127054591684 chr21 48129895 650455480 13.514583399776791 67.09720762742599 chr22 51304566 606461500 11.820809477269528 69.12695693003579 chrMT 16571 31977728 1929.7403898376683 242.22722350286872 chrX 155270560 1205086645 7.761204989535686 25.098716448808702 chrY 59373566 476401606 8.023799783223396 153.01521871516243