BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926923.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 14,031,686 number of mapped reads = 12,761,334 (90.95%) number of supplementary alignments = 418,361 (2.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,382,262 number of mapped paired reads (second in pair) = 6,379,072 number of mapped paired reads (both in pair) = 12,499,304 number of mapped paired reads (singletons) = 262,030 number of mapped bases = 1,130,281,793 bp number of sequenced bases = 1,129,382,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 959,975 duplication rate = 6.2% >>>>>>> Insert size mean insert size = 324,077.9342 std insert size = 5,569,318.8469 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 52.4543 >>>>>>> ACTG content number of A's = 321,538,577 bp (28.47%) number of C's = 213,984,641 bp (18.95%) number of T's = 331,010,219 bp (29.31%) number of G's = 262,794,061 bp (23.27%) number of N's = 54,540 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 10,878,836 number of insertions = 199,613 mapped reads with insertion percentage = 1.53% number of deletions = 607,311 mapped reads with deletion percentage = 4.64% homopolymer indels = 51.86% >>>>>>> Coverage mean coverageData = 0.3651X std coverageData = 1.4135X There is a 20.56% of reference with a coverageData >= 1X There is a 8.31% of reference with a coverageData >= 2X There is a 3.49% of reference with a coverageData >= 3X There is a 1.67% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.16% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 91404067 0.3667155035894575 1.4372829417748383 chr2 243199373 97215439 0.399735565930098 2.688150786921624 chr3 198022430 76679260 0.3872251239417676 0.9547197197089227 chr4 191154276 69584427 0.3640223407819556 1.2173959599241895 chr5 180915260 69816072 0.38590482638114665 0.9531870716836268 chr6 171115067 65559527 0.3831312353107982 1.6386521014625153 chr7 159138663 58868237 0.36991788098659595 1.1936265211843313 chr8 146364022 57579467 0.39339904857219626 1.061859962656975 chr9 141213431 48007266 0.3399624643352798 1.648113300755588 chr10 135534747 53962135 0.39814244091959683 1.6902895112132021 chr11 135006516 54281629 0.4020667343196976 1.2398246581328345 chr12 133851895 51281067 0.3831179752815603 1.0047724885527685 chr13 115169878 33590030 0.2916563825829528 0.826200819254885 chr14 107349540 34562248 0.3219599077928047 0.9013023767922913 chr15 102531392 33954660 0.3311635523294173 0.908464363397639 chr16 90354753 33776193 0.3738175566702064 1.6609295500552137 chr17 81195210 28443229 0.3503067360747019 0.9754521206490899 chr18 78077248 30157366 0.3862503709147126 1.395978986701727 chr19 59128983 18669185 0.3157366160009889 1.1921675698315302 chr20 63025520 25538651 0.40521126997444845 1.0319753945102437 chr21 48129895 14447580 0.30017892206081065 1.152383532451733 chr22 51304566 13272650 0.25870309476938175 0.8402578151627407 chrMT 16571 901373 54.394605032888784 43.482854921078264 chrX 155270560 66688055 0.4294958104099064 1.0694217653080411 chrY 59373566 2041980 0.034392072728122815 1.102968937304241