BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975236.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 46,252,408 number of mapped reads = 46,160,775 (99.8%) number of supplementary alignments = 174,807 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,084,630 number of mapped paired reads (second in pair) = 23,076,145 number of mapped paired reads (both in pair) = 46,096,502 number of mapped paired reads (singletons) = 64,273 number of mapped bases = 4,384,030,797 bp number of sequenced bases = 4,382,284,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,382,245 duplication rate = 45.59% >>>>>>> Insert size mean insert size = 158,423.8941 std insert size = 3,921,275.6817 median insert size = 236 >>>>>>> Mapping quality mean mapping quality = 56.1047 >>>>>>> ACTG content number of A's = 1,157,104,580 bp (26.4%) number of C's = 1,008,296,691 bp (23.01%) number of T's = 1,181,635,239 bp (26.96%) number of G's = 1,035,123,900 bp (23.62%) number of N's = 123,645 bp (0%) GC percentage = 46.63% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 31,794,956 number of insertions = 447,280 mapped reads with insertion percentage = 0.95% number of deletions = 1,198,796 mapped reads with deletion percentage = 2.55% homopolymer indels = 48.03% >>>>>>> Coverage mean coverageData = 1.4162X std coverageData = 23.3491X There is a 8.68% of reference with a coverageData >= 1X There is a 4.34% of reference with a coverageData >= 2X There is a 2.81% of reference with a coverageData >= 3X There is a 2.24% of reference with a coverageData >= 4X There is a 1.94% of reference with a coverageData >= 5X There is a 1.77% of reference with a coverageData >= 6X There is a 1.64% of reference with a coverageData >= 7X There is a 1.55% of reference with a coverageData >= 8X There is a 1.47% of reference with a coverageData >= 9X There is a 1.41% of reference with a coverageData >= 10X There is a 1.35% of reference with a coverageData >= 11X There is a 1.3% of reference with a coverageData >= 12X There is a 1.26% of reference with a coverageData >= 13X There is a 1.22% of reference with a coverageData >= 14X There is a 1.18% of reference with a coverageData >= 15X There is a 1.14% of reference with a coverageData >= 16X There is a 1.11% of reference with a coverageData >= 17X There is a 1.08% of reference with a coverageData >= 18X There is a 1.05% of reference with a coverageData >= 19X There is a 1.02% of reference with a coverageData >= 20X There is a 1% of reference with a coverageData >= 21X There is a 0.97% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.93% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.89% of reference with a coverageData >= 26X There is a 0.87% of reference with a coverageData >= 27X There is a 0.85% of reference with a coverageData >= 28X There is a 0.83% of reference with a coverageData >= 29X There is a 0.82% of reference with a coverageData >= 30X There is a 0.8% of reference with a coverageData >= 31X There is a 0.79% of reference with a coverageData >= 32X There is a 0.77% of reference with a coverageData >= 33X There is a 0.76% of reference with a coverageData >= 34X There is a 0.74% of reference with a coverageData >= 35X There is a 0.73% of reference with a coverageData >= 36X There is a 0.72% of reference with a coverageData >= 37X There is a 0.71% of reference with a coverageData >= 38X There is a 0.69% of reference with a coverageData >= 39X There is a 0.68% of reference with a coverageData >= 40X There is a 0.67% of reference with a coverageData >= 41X There is a 0.66% of reference with a coverageData >= 42X There is a 0.65% of reference with a coverageData >= 43X There is a 0.64% of reference with a coverageData >= 44X There is a 0.63% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.61% of reference with a coverageData >= 47X There is a 0.6% of reference with a coverageData >= 48X There is a 0.59% of reference with a coverageData >= 49X There is a 0.58% of reference with a coverageData >= 50X There is a 0.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 387728344 1.5555762406706302 22.481181684469142 chr2 243199373 392622023 1.6144039277601263 23.448256411612046 chr3 198022430 246426169 1.2444356379224313 20.054106609597834 chr4 191154276 132328976 0.6922627040788771 13.3297540283317 chr5 180915260 195279229 1.0793961161706316 18.414061489494546 chr6 171115067 218780591 1.2785583107067948 22.216214192870183 chr7 159138663 160531879 1.008754729829545 19.416631172354474 chr8 146364022 150234887 1.0264468340450497 17.538177365112 chr9 141213431 180148849 1.275720359772294 20.664000471883103 chr10 135534747 179861787 1.3270529586040398 22.69408609938043 chr11 135006516 341659946 2.5306922667347402 34.7991856709726 chr12 133851895 308464238 2.304519020817748 31.415584059208772 chr13 115169878 66630128 0.5785378013511484 11.394551526523514 chr14 107349540 151199333 1.4084767666447382 21.63542667947853 chr15 102531392 121531590 1.1853110313766149 20.16701437327852 chr16 90354753 119640461 1.3241191750034444 19.873441187457942 chr17 81195210 233277777 2.8730485086497097 33.981607963418924 chr18 78077248 89019581 1.1401475241545398 18.890057979581176 chr19 59128983 227540580 3.8482072319762373 45.86428613801408 chr20 63025520 273960773 4.346822890156242 54.48462491898606 chr21 48129895 31382906 0.652046010073365 12.773894961846988 chr22 51304566 66408694 1.294401242961494 19.384206518897525 chrMT 16571 106705 6.439261360207592 10.911412870230766 chrX 155270560 98846929 0.6366108874728088 14.16623818010577 chrY 59373566 10418422 0.1754723979354718 5.9347682505136765