BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094045.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 377,262 number of mapped reads = 361,564 (95.84%) number of supplementary alignments = 14,354 (3.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 181,629 number of mapped paired reads (second in pair) = 179,935 number of mapped paired reads (both in pair) = 358,974 number of mapped paired reads (singletons) = 2,590 number of mapped bases = 47,859,009 bp number of sequenced bases = 46,618,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 337,237 duplication rate = 49.94% >>>>>>> Insert size mean insert size = 662,759.6197 std insert size = 7,356,451.2344 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 44.848 >>>>>>> ACTG content number of A's = 12,909,661 bp (27.69%) number of C's = 10,449,875 bp (22.42%) number of T's = 12,415,390 bp (26.63%) number of G's = 10,842,722 bp (23.26%) number of N's = 666 bp (0%) GC percentage = 45.67% >>>>>>> Mismatches and indels general error rate = 0.0446 number of mismatches = 2,042,870 number of insertions = 28,569 mapped reads with insertion percentage = 7.73% number of deletions = 164,706 mapped reads with deletion percentage = 42.36% homopolymer indels = 29.14% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 3.4224X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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% 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 772447 0.003099077534494889 1.234640998991593 chr2 243199373 2046760 0.00841597564480563 2.399435595399521 chr3 198022430 1139726 0.005755539915352013 1.5595752496739166 chr4 191154276 1803985 0.009437324854820408 2.9636168491977446 chr5 180915260 447353 0.0024727212066024723 0.775492520749102 chr6 171115067 1392137 0.008135677497061086 3.272381232505513 chr7 159138663 1408334 0.008849728742536941 2.294284103638555 chr8 146364022 972251 0.006642691193604942 1.7812414782466786 chr9 141213431 738680 0.005230947189435543 2.208209135548588 chr10 135534747 1200947 0.008860805266416295 2.7620686668928904 chr11 135006516 1592508 0.011795786212274376 3.119749757408342 chr12 133851895 1663847 0.012430507614404711 3.2549355355858203 chr13 115169878 1045147 0.009074829444553201 2.4182497128730573 chr14 107349540 259095 0.0024135641382347795 0.7696126350302598 chr15 102531392 775940 0.007567828592437329 1.8791591141577668 chr16 90354753 295942 0.003275334060179435 0.9882348432929281 chr17 81195210 776567 0.009564197198332266 2.234723736356023 chr18 78077248 263957 0.003380715980153399 0.9501551068485473 chr19 59128983 191782 0.0032434516927172586 0.6996114128001407 chr20 63025520 277079 0.004396298515268101 0.937430996046231 chr21 48129895 80029 0.0016627711321622455 0.37689583342337163 chr22 51304566 115836 0.0022578107375472193 0.5514818269923414 chrMT 16571 2342335 141.3514573652767 585.992907819474 chrX 155270560 25944083 0.16708951780685277 10.352335837960581 chrY 59373566 312242 0.005258939643274921 1.7643366856990201