BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472776.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,125,804 number of mapped reads = 15,992,746 (99.17%) number of supplementary alignments = 53,253 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,018,232 number of mapped paired reads (second in pair) = 7,974,514 number of mapped paired reads (both in pair) = 15,914,812 number of mapped paired reads (singletons) = 77,934 number of mapped bases = 1,572,670,511 bp number of sequenced bases = 1,572,459,465 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,764,816 duplication rate = 45.57% >>>>>>> Insert size mean insert size = 22,880.4556 std insert size = 1,502,606.62 median insert size = 226 >>>>>>> Mapping quality mean mapping quality = 55.1307 >>>>>>> ACTG content number of A's = 421,493,217 bp (26.8%) number of C's = 367,566,088 bp (23.38%) number of T's = 418,818,453 bp (26.63%) number of G's = 364,276,419 bp (23.17%) number of N's = 305,288 bp (0.02%) GC percentage = 46.54% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 9,268,647 number of insertions = 93,285 mapped reads with insertion percentage = 0.58% number of deletions = 81,382 mapped reads with deletion percentage = 0.5% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.508X std coverageData = 16.4268X There is a 5.01% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.25% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 181911598 0.7298340813361505 21.785638906525662 chr2 243199373 99487947 0.4090797840996079 13.202460677709983 chr3 198022430 173320752 0.8752581816110427 20.55504901244426 chr4 191154276 53161826 0.27810953075410144 10.013997871092833 chr5 180915260 75149837 0.41538694414169375 12.252586016621073 chr6 171115067 110523322 0.6459005857152251 22.417857341043923 chr7 159138663 68934018 0.43316951833383194 13.972380991238003 chr8 146364022 78738260 0.5379618496682197 16.410544695591454 chr9 141213431 97764663 0.6923184452617683 20.039572135195577 chr10 135534747 49156326 0.36268430854856726 21.397430961972006 chr11 135006516 73182170 0.542063984526495 16.699652600117698 chr12 133851895 76343446 0.5703576030806288 16.338708711431227 chr13 115169878 26865641 0.23326968358862027 7.803228493528079 chr14 107349540 36258144 0.33775779570177944 11.611732500598631 chr15 102531392 39164910 0.38197969652065195 10.56676793374326 chr16 90354753 56789323 0.6285150599659102 17.72858516442494 chr17 81195210 64494319 0.7943118688898028 20.056237342255645 chr18 78077248 26741443 0.34249981505495686 12.003163333023707 chr19 59128983 33108248 0.5599326475816436 14.009233905526372 chr20 63025520 41114065 0.652339956893652 18.30390122146333 chr21 48129895 8038921 0.1670255254037018 6.118981535886652 chr22 51304566 30282442 0.5902484780789297 19.828401206416345 chrMT 16571 4616 0.2785589282481443 0.7906952391851644 chrX 155270560 69552801 0.44794583725337245 15.197675405737353 chrY 59373566 2581473 0.04347849007418554 1.4460518041757016