BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354869.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 29,219,686 number of mapped reads = 28,914,575 (98.96%) number of supplementary alignments = 1,230,881 (4.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,469,755 number of mapped paired reads (second in pair) = 14,444,820 number of mapped paired reads (both in pair) = 28,868,528 number of mapped paired reads (singletons) = 46,047 number of mapped bases = 3,580,246,417 bp number of sequenced bases = 3,578,572,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,269,032 duplication rate = 67.53% >>>>>>> Insert size mean insert size = 434,376.4157 std insert size = 7,658,101.8648 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 53.6939 >>>>>>> ACTG content number of A's = 992,869,940 bp (27.74%) number of C's = 763,077,456 bp (21.32%) number of T's = 1,014,169,490 bp (28.34%) number of G's = 808,423,276 bp (22.59%) number of N's = 31,903 bp (0%) GC percentage = 43.91% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 19,245,358 number of insertions = 569,747 mapped reads with insertion percentage = 1.85% number of deletions = 603,547 mapped reads with deletion percentage = 1.99% homopolymer indels = 44.48% >>>>>>> Coverage mean coverageData = 1.1565X std coverageData = 63.8634X There is a 26.82% of reference with a coverageData >= 1X There is a 22.89% of reference with a coverageData >= 2X There is a 14.85% of reference with a coverageData >= 3X There is a 12.67% of reference with a coverageData >= 4X There is a 7.94% of reference with a coverageData >= 5X There is a 6.82% of reference with a coverageData >= 6X There is a 4.21% of reference with a coverageData >= 7X There is a 3.63% of reference with a coverageData >= 8X There is a 2.23% of reference with a coverageData >= 9X There is a 1.91% of reference with a coverageData >= 10X There is a 1.18% of reference with a coverageData >= 11X There is a 1% of reference with a coverageData >= 12X There is a 0.62% of reference with a coverageData >= 13X There is a 0.53% of reference with a coverageData >= 14X There is a 0.34% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.19% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 290283215 1.1646238385901555 32.420083167076925 chr2 243199373 353369359 1.4530027550687805 221.50012160634256 chr3 198022430 232208470 1.1726372108452563 3.2801326427433595 chr4 191154276 236081846 1.2350330368754083 13.578957407622669 chr5 180915260 204947185 1.1328352566831565 2.577399998210788 chr6 171115067 201364308 1.1767771916893794 5.391392200909784 chr7 159138663 200397639 1.259264312155243 20.39649759381527 chr8 146364022 177040980 1.2095935707478713 6.721964116772417 chr9 141213431 153016457 1.0835828852568563 18.110075895688404 chr10 135534747 194133156 1.4323497132436451 36.83159493910423 chr11 135006516 165795387 1.2280547036707472 6.674867409949235 chr12 133851895 155753671 1.1636269400593844 2.6351718471583006 chr13 115169878 111787590 0.970632182140542 2.3115315994048946 chr14 107349540 108537112 1.0110626650100225 8.542330320725881 chr15 102531392 100145417 0.9767293220792321 2.323830232855718 chr16 90354753 112479959 1.2448704165014983 6.8859973288471705 chr17 81195210 101205653 1.246448565130874 7.115470446437901 chr18 78077248 96796738 1.2397560170153539 15.031554186221696 chr19 59128983 72566762 1.2272621364044094 17.261581310128406 chr20 63025520 77777867 1.2340694214026318 5.141001059102422 chr21 48129895 49144564 1.0210818868397697 7.531769384268888 chr22 51304566 46986225 0.9158293045496184 3.771108960822405 chrMT 16571 4499685 271.5397380966749 58.605906717566626 chrX 155270560 95263740 0.6135338212214859 2.8818247028153734 chrY 59373566 38663432 0.6511893188291907 17.439414327212344