BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238648.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,606,269 number of mapped reads = 3,099,461 (85.95%) number of supplementary alignments = 26,048 (0.72%) number of secondary alignments = 0 number of mapped bases = 191,466,251 bp number of sequenced bases = 191,379,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,117,996 duplication rate = 21.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3081 >>>>>>> ACTG content number of A's = 46,307,752 bp (24.2%) number of C's = 33,811,267 bp (17.67%) number of T's = 64,823,140 bp (33.87%) number of G's = 46,432,713 bp (24.26%) number of N's = 4,492 bp (0%) GC percentage = 41.93% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,052,506 number of insertions = 12,580 mapped reads with insertion percentage = 0.4% number of deletions = 51,841 mapped reads with deletion percentage = 1.66% homopolymer indels = 41.87% >>>>>>> Coverage mean coverageData = 0.0618X std coverageData = 1.156X There is a 2.08% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.29% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20747114 0.08323796312627843 0.8081657372596196 chr2 243199373 3508277 0.014425518276315621 2.945894741518936 chr3 198022430 8516709 0.043008809658582614 0.5248542818834945 chr4 191154276 2564679 0.013416801620487945 0.24887033430263314 chr5 180915260 12146263 0.06713785780149226 0.6322415340758066 chr6 171115067 32026118 0.18716129772488124 1.5286833486831983 chr7 159138663 14384616 0.09039045401556503 1.307098451441964 chr8 146364022 5272568 0.03602366160722203 0.5898760393856858 chr9 141213431 1470552 0.010413683667242673 0.3136637560627286 chr10 135534747 13564242 0.1000794430966105 0.8328353019785272 chr11 135006516 8340301 0.06177702563630336 0.650132886711928 chr12 133851895 12601809 0.09414740822309613 0.7494788466053971 chr13 115169878 6948407 0.060331808287580196 0.7976393230720853 chr14 107349540 4464645 0.041589791628357235 0.5066134959082755 chr15 102531392 6977951 0.06805672744597088 0.8175996527825993 chr16 90354753 10178061 0.11264555169554832 0.8514912452376582 chr17 81195210 1703459 0.02097979671460915 0.342763312009502 chr18 78077248 2463359 0.031550279538541115 2.135227195561759 chr19 59128983 915683 0.015486195661440685 0.4166380129328414 chr20 63025520 12569277 0.19943154772860264 1.1353999430490678 chr21 48129895 2199477 0.045698769964073266 0.5188054638677423 chr22 51304566 437789 0.008533139136193062 0.18540390426146977 chrMT 16571 17865 1.0780882264196487 2.2278907230589406 chrX 155270560 5636190 0.03629915419896727 0.4522275345226725 chrY 59373566 1810840 0.030499094496025385 0.5277696442425673