BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926915.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,750,560 number of mapped reads = 31,584,414 (96.44%) number of supplementary alignments = 1,135,536 (3.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,855,034 number of mapped paired reads (second in pair) = 15,729,380 number of mapped paired reads (both in pair) = 31,049,476 number of mapped paired reads (singletons) = 534,938 number of mapped bases = 2,889,182,218 bp number of sequenced bases = 2,886,904,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,067,585 duplication rate = 7.73% >>>>>>> Insert size mean insert size = 415,145.8289 std insert size = 6,325,561.0709 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 51.4797 >>>>>>> ACTG content number of A's = 824,898,252 bp (28.57%) number of C's = 564,514,700 bp (19.55%) number of T's = 830,592,261 bp (28.77%) number of G's = 666,683,393 bp (23.09%) number of N's = 215,913 bp (0.01%) GC percentage = 42.65% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 27,968,319 number of insertions = 487,351 mapped reads with insertion percentage = 1.52% number of deletions = 1,562,620 mapped reads with deletion percentage = 4.82% homopolymer indels = 52.26% >>>>>>> Coverage mean coverageData = 0.9333X std coverageData = 3.2396X There is a 35.19% of reference with a coverageData >= 1X There is a 20.02% of reference with a coverageData >= 2X There is a 11.95% of reference with a coverageData >= 3X There is a 7.62% of reference with a coverageData >= 4X There is a 5.04% of reference with a coverageData >= 5X There is a 3.43% of reference with a coverageData >= 6X There is a 2.39% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.22% of reference with a coverageData >= 9X There is a 0.89% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 244846929 0.9823322727047489 3.3381146191665074 chr2 243199373 253266171 1.0413931905983984 4.15489731094556 chr3 198022430 200624690 1.0131412385960519 2.0659814166208226 chr4 191154276 177684166 0.9295327822015345 2.193443262520242 chr5 180915260 179215308 0.9906036008239437 1.975369126792334 chr6 171115067 171094205 0.99987808203938 2.306216163762459 chr7 159138663 153430439 0.964130501712208 2.327185474542796 chr8 146364022 150348142 1.0272206239317474 2.192897231009519 chr9 141213431 125482080 0.888598762252296 2.712876495064657 chr10 135534747 147722793 1.0899256188525588 9.386303876252109 chr11 135006516 142088049 1.0524532682555856 2.280065998553387 chr12 133851895 134996141 1.008548597687018 2.487444620764794 chr13 115169878 89932514 0.7808683621250341 1.8623001253727667 chr14 107349540 89835791 0.8368530596404977 1.8868082135523243 chr15 102531392 88383025 0.8620094126879697 2.00633871016092 chr16 90354753 4363635 0.04829447101692592 1.8466921378202386 chr17 81195210 77786384 0.9580169076476309 2.227334172935303 chr18 78077248 78035810 0.9994692692037507 2.488168843390306 chr19 59128983 95467356 1.6145611028013116 3.475045209431366 chr20 63025520 70439528 1.1176350151494188 2.2836175811986057 chr21 48129895 35985543 0.7476754935783675 2.491505582965304 chr22 51304566 1515961 0.029548266717625095 0.581216895356948 chrMT 16571 3891753 234.85323758373062 148.7697646581354 chrX 155270560 168929470 1.0879684468195387 2.1412539992618553 chrY 59373566 3816335 0.06427666817249952 1.3943022222605856