BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472800.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 = 114,517,230 number of mapped reads = 113,969,470 (99.52%) number of supplementary alignments = 87,098 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 57,169,951 number of mapped paired reads (second in pair) = 56,799,519 number of mapped paired reads (both in pair) = 113,557,246 number of mapped paired reads (singletons) = 412,224 number of mapped bases = 11,291,093,629 bp number of sequenced bases = 11,289,670,669 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,322,312 duplication rate = 47.68% >>>>>>> Insert size mean insert size = 13,745.4023 std insert size = 1,158,902.361 median insert size = 241 >>>>>>> Mapping quality mean mapping quality = 53.6609 >>>>>>> ACTG content number of A's = 3,177,344,093 bp (28.14%) number of C's = 2,465,803,054 bp (21.84%) number of T's = 3,222,864,420 bp (28.55%) number of G's = 2,422,531,123 bp (21.46%) number of N's = 1,127,979 bp (0.01%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 46,709,797 number of insertions = 507,412 mapped reads with insertion percentage = 0.44% number of deletions = 601,993 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 3.6474X std coverageData = 26.1279X There is a 17.96% of reference with a coverageData >= 1X There is a 9.82% of reference with a coverageData >= 2X There is a 6.33% of reference with a coverageData >= 3X There is a 5.41% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 4.54% of reference with a coverageData >= 6X There is a 4.33% of reference with a coverageData >= 7X There is a 4.18% of reference with a coverageData >= 8X There is a 4.04% of reference with a coverageData >= 9X There is a 3.93% of reference with a coverageData >= 10X There is a 3.83% of reference with a coverageData >= 11X There is a 3.73% of reference with a coverageData >= 12X There is a 3.64% of reference with a coverageData >= 13X There is a 3.56% of reference with a coverageData >= 14X There is a 3.48% of reference with a coverageData >= 15X There is a 3.41% of reference with a coverageData >= 16X There is a 3.34% of reference with a coverageData >= 17X There is a 3.28% of reference with a coverageData >= 18X There is a 3.21% of reference with a coverageData >= 19X There is a 3.15% of reference with a coverageData >= 20X There is a 3.1% of reference with a coverageData >= 21X There is a 3.04% of reference with a coverageData >= 22X There is a 2.99% of reference with a coverageData >= 23X There is a 2.94% of reference with a coverageData >= 24X There is a 2.89% of reference with a coverageData >= 25X There is a 2.84% of reference with a coverageData >= 26X There is a 2.79% of reference with a coverageData >= 27X There is a 2.75% of reference with a coverageData >= 28X There is a 2.7% of reference with a coverageData >= 29X There is a 2.66% of reference with a coverageData >= 30X There is a 2.62% of reference with a coverageData >= 31X There is a 2.58% of reference with a coverageData >= 32X There is a 2.54% of reference with a coverageData >= 33X There is a 2.5% of reference with a coverageData >= 34X There is a 2.47% of reference with a coverageData >= 35X There is a 2.43% of reference with a coverageData >= 36X There is a 2.4% of reference with a coverageData >= 37X There is a 2.36% of reference with a coverageData >= 38X There is a 2.33% of reference with a coverageData >= 39X There is a 2.3% of reference with a coverageData >= 40X There is a 2.26% of reference with a coverageData >= 41X There is a 2.23% of reference with a coverageData >= 42X There is a 2.2% of reference with a coverageData >= 43X There is a 2.17% of reference with a coverageData >= 44X There is a 2.14% of reference with a coverageData >= 45X There is a 2.12% of reference with a coverageData >= 46X There is a 2.09% of reference with a coverageData >= 47X There is a 2.06% of reference with a coverageData >= 48X There is a 2.03% of reference with a coverageData >= 49X There is a 2.01% of reference with a coverageData >= 50X There is a 1.98% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1082634458 4.343557715749884 29.07272163134949 chr2 243199373 1101458512 4.529035163260885 32.62624990267162 chr3 198022430 770526387 3.8911066135285783 26.413150523980743 chr4 191154276 452458915 2.3669829651103385 18.442610546106607 chr5 180915260 480707166 2.6570846815243776 19.316649144699223 chr6 171115067 637215146 3.723898527299177 25.911496176738876 chr7 159138663 689734167 4.334170929914121 31.57969442963098 chr8 146364022 460367293 3.1453583108012704 23.851686285812242 chr9 141213431 674964212 4.779745150445357 34.55519581487662 chr10 135534747 449412219 3.315845043042726 23.4423860773448 chr11 135006516 377846640 2.798728914684385 17.322084745637373 chr12 133851895 518865858 3.8764177227375076 23.081532458953 chr13 115169878 355907293 3.0902810629008393 26.974532652140827 chr14 107349540 219070725 2.0407234628112985 14.845377708128783 chr15 102531392 243727824 2.377104409155003 15.486780772747561 chr16 90354753 450473492 4.985609246256254 31.544221703183737 chr17 81195210 409469882 5.043030026032324 24.380154139908633 chr18 78077248 121712662 1.5588748978447602 12.635500404023226 chr19 59128983 468913282 7.930345800129862 34.48202824837611 chr20 63025520 499640901 7.927596646564757 48.50691855566972 chr21 48129895 138256470 2.872569532927508 25.197635750629704 chr22 51304566 172204820 3.356520353373616 21.262497476560682 chrMT 16571 1836449 110.82306438959628 306.6345526815705 chrX 155270560 471492408 3.0365859954391867 24.41417855958701 chrY 59373566 42196448 0.7106941833340447 10.6956138342772