BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617376.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 27,985,361 (87.45%) number of supplementary alignments = 60,814 (0.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,380,099 number of mapped paired reads (second in pair) = 13,605,262 number of mapped paired reads (both in pair) = 26,846,328 number of mapped paired reads (singletons) = 1,139,033 number of mapped bases = 2,726,595,716 bp number of sequenced bases = 2,725,822,441 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,368,461 duplication rate = 1.44% >>>>>>> Insert size mean insert size = 49,007.7909 std insert size = 2,106,810.8297 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.1633 >>>>>>> ACTG content number of A's = 829,707,019 bp (30.44%) number of C's = 538,087,803 bp (19.74%) number of T's = 815,370,610 bp (29.91%) number of G's = 541,100,228 bp (19.85%) number of N's = 1,556,781 bp (0.06%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.018 number of mismatches = 48,338,823 number of insertions = 275,266 mapped reads with insertion percentage = 0.95% number of deletions = 326,274 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.37% >>>>>>> Coverage mean coverageData = 0.8808X std coverageData = 8.6269X There is a 50.28% of reference with a coverageData >= 1X There is a 21.67% of reference with a coverageData >= 2X There is a 7.98% of reference with a coverageData >= 3X There is a 2.71% of reference with a coverageData >= 4X There is a 0.91% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 177109954 0.7105697602253918 17.730573308927106 chr2 243199373 269564593 1.1084099012048028 7.635537131643677 chr3 198022430 218843546 1.1051452403649424 1.4270912989008633 chr4 191154276 150223698 0.7858767334087782 7.479055921091664 chr5 180915260 172172495 0.9516748062048497 1.3781897007202755 chr6 171115067 128517461 0.7510587071797716 3.368163791161834 chr7 159138663 221973731 1.3948447650336235 10.078017014582635 chr8 146364022 115042606 0.7860033116608397 6.667056760568538 chr9 141213431 114346453 0.8097420492530912 12.49472572911131 chr10 135534747 114213262 0.842686207987683 18.145294282160283 chr11 135006516 146085051 1.0820592614952007 4.855617164197835 chr12 133851895 120604040 0.9010260183466211 1.2651785108923244 chr13 115169878 120159589 1.043324791921721 1.2397147087678615 chr14 107349540 78792487 0.7339806672669487 1.2967979584441738 chr15 102531392 61018173 0.5951169862201813 0.9301461279892824 chr16 90354753 67901491 0.7514988281800737 7.543734760776792 chr17 81195210 82873030 1.0206640268557714 6.175626921310628 chr18 78077248 48837405 0.6255011062889921 13.15904486197495 chr19 59128983 49319750 0.83410448645802 8.725580039219036 chr20 63025520 77058643 1.2226577900507605 2.181023662386506 chr21 48129895 43218209 0.8979493722145041 2.842442974581394 chr22 51304566 23540850 0.45884512501284974 0.8546142611735708 chrMT 16571 1804329 108.88473839840685 22.957873293470232 chrX 155270560 114571519 0.7378830797029392 2.73681564746009 chrY 59373566 8803351 0.14827054517830376 6.845437513888102