BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16352027.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 593,065,306 number of mapped reads = 543,248,702 (91.6%) number of supplementary alignments = 24,918,992 (4.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 273,381,645 number of mapped paired reads (second in pair) = 269,867,057 number of mapped paired reads (both in pair) = 538,187,212 number of mapped paired reads (singletons) = 5,061,490 number of mapped bases = 75,381,833,491 bp number of sequenced bases = 75,317,762,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,052,816 duplication rate = 34.29% >>>>>>> Insert size mean insert size = 155,545.4628 std insert size = 3,831,043.9165 median insert size = 238 >>>>>>> Mapping quality mean mapping quality = 53.769 >>>>>>> ACTG content number of A's = 21,707,991,040 bp (28.82%) number of C's = 15,905,223,099 bp (21.12%) number of T's = 21,578,515,589 bp (28.65%) number of G's = 16,120,256,541 bp (21.4%) number of N's = 5,776,698 bp (0.01%) GC percentage = 42.52% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 652,317,871 number of insertions = 12,647,231 mapped reads with insertion percentage = 2.21% number of deletions = 35,995,930 mapped reads with deletion percentage = 6.36% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 24.3505X std coverageData = 246.5427X There is a 91.69% of reference with a coverageData >= 1X There is a 91.6% of reference with a coverageData >= 2X There is a 91.52% of reference with a coverageData >= 3X There is a 91.44% of reference with a coverageData >= 4X There is a 91.33% of reference with a coverageData >= 5X There is a 91.17% of reference with a coverageData >= 6X There is a 90.94% of reference with a coverageData >= 7X There is a 90.6% of reference with a coverageData >= 8X There is a 90.11% of reference with a coverageData >= 9X There is a 89.44% of reference with a coverageData >= 10X There is a 88.54% of reference with a coverageData >= 11X There is a 87.37% of reference with a coverageData >= 12X There is a 85.89% of reference with a coverageData >= 13X There is a 84.07% of reference with a coverageData >= 14X There is a 81.9% of reference with a coverageData >= 15X There is a 79.36% of reference with a coverageData >= 16X There is a 76.48% of reference with a coverageData >= 17X There is a 73.27% of reference with a coverageData >= 18X There is a 69.76% of reference with a coverageData >= 19X There is a 66% of reference with a coverageData >= 20X There is a 62.04% of reference with a coverageData >= 21X There is a 57.94% of reference with a coverageData >= 22X There is a 53.76% of reference with a coverageData >= 23X There is a 49.55% of reference with a coverageData >= 24X There is a 45.38% of reference with a coverageData >= 25X There is a 41.29% of reference with a coverageData >= 26X There is a 37.34% of reference with a coverageData >= 27X There is a 33.56% of reference with a coverageData >= 28X There is a 29.99% of reference with a coverageData >= 29X There is a 26.64% of reference with a coverageData >= 30X There is a 23.54% of reference with a coverageData >= 31X There is a 20.69% of reference with a coverageData >= 32X There is a 18.1% of reference with a coverageData >= 33X There is a 15.75% of reference with a coverageData >= 34X There is a 13.65% of reference with a coverageData >= 35X There is a 11.78% of reference with a coverageData >= 36X There is a 10.13% of reference with a coverageData >= 37X There is a 8.68% of reference with a coverageData >= 38X There is a 7.42% of reference with a coverageData >= 39X There is a 6.32% of reference with a coverageData >= 40X There is a 5.38% of reference with a coverageData >= 41X There is a 4.57% of reference with a coverageData >= 42X There is a 3.88% of reference with a coverageData >= 43X There is a 3.3% of reference with a coverageData >= 44X There is a 2.8% of reference with a coverageData >= 45X There is a 2.38% of reference with a coverageData >= 46X There is a 2.03% of reference with a coverageData >= 47X There is a 1.74% of reference with a coverageData >= 48X There is a 1.49% of reference with a coverageData >= 49X There is a 1.29% of reference with a coverageData >= 50X There is a 1.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6111747156 24.520489182652828 549.5515410284503 chr2 243199373 6450324829 26.522785603563214 217.53274147970416 chr3 198022430 4936806009 24.930539479795293 26.277430511843793 chr4 191154276 4901968382 25.64404252196796 180.1979856102145 chr5 180915260 4509940097 24.928467045842346 19.72569632122308 chr6 171115067 4277040489 24.99511331167582 68.10142020531417 chr7 159138663 4059688335 25.51038357661708 185.14134595730488 chr8 146364022 3772264831 25.77317006907613 347.60644503211836 chr9 141213431 3254258552 23.044964837657687 276.12466213295977 chr10 135534747 3889955615 28.70079961856571 524.4620863750052 chr11 135006516 3413539188 25.284255079954807 105.55575859178988 chr12 133851895 3309349859 24.723967180292817 16.266025300249293 chr13 115169878 2371854466 20.59439939668947 14.334244366912806 chr14 107349540 2238252246 20.85013355436828 22.824209987453063 chr15 102531392 2067775420 20.16724224323415 14.304005703770398 chr16 90354753 2411628588 26.69066659946489 197.59505956277283 chr17 81195210 2090455803 25.746048356793462 122.14520653731545 chr18 78077248 2048209644 26.233117796364954 273.29127734725034 chr19 59128983 1528717175 25.853939936697373 310.0227374771862 chr20 63025520 1567230402 24.866600101038436 51.191869528980675 chr21 48129895 1024776890 21.291899556398366 80.99248729745736 chr22 51304566 912881307 17.793373537162363 21.725622894752888 chrMT 16571 154330321 9313.277472693258 1314.1126288411103 chrX 155270560 3832077895 24.680003054023892 56.44364709943031 chrY 59373566 246759992 4.156058135366166 209.23535620423112