BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094062.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 = 434,364 number of mapped reads = 401,472 (92.43%) number of supplementary alignments = 22,606 (5.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 201,819 number of mapped paired reads (second in pair) = 199,653 number of mapped paired reads (both in pair) = 397,634 number of mapped paired reads (singletons) = 3,838 number of mapped bases = 52,444,655 bp number of sequenced bases = 51,457,270 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,884 duplication rate = 47.65% >>>>>>> Insert size mean insert size = 1,235,497.9113 std insert size = 10,082,297.0676 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 47.9096 >>>>>>> ACTG content number of A's = 14,261,560 bp (27.72%) number of C's = 11,556,745 bp (22.46%) number of T's = 13,563,544 bp (26.36%) number of G's = 12,074,986 bp (23.47%) number of N's = 435 bp (0%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.0354 number of mismatches = 1,770,206 number of insertions = 27,757 mapped reads with insertion percentage = 6.82% number of deletions = 138,817 mapped reads with deletion percentage = 33.36% homopolymer indels = 29.75% >>>>>>> Coverage mean coverageData = 0.0169X std coverageData = 3.3029X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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 789547 0.0031676831810180323 0.813127962164787 chr2 243199373 2734876 0.011245407281539332 2.7611534378123874 chr3 198022430 860734 0.004346649013447618 0.993510819764709 chr4 191154276 1378218 0.007209977348348723 1.7058395554894663 chr5 180915260 845703 0.004674580795450864 1.4104442188649036 chr6 171115067 1219822 0.007128665063725803 2.0397782451966537 chr7 159138663 1240228 0.00779337953844692 1.8523422197883894 chr8 146364022 1035475 0.007074655272864803 1.9877920693708093 chr9 141213431 648860 0.0045948887114002634 1.3326721512752338 chr10 135534747 935841 0.006904805009153852 1.5058016971262205 chr11 135006516 1269145 0.009400620337465786 1.9056454436591277 chr12 133851895 1458445 0.010895960793084027 2.2673711764379196 chr13 115169878 1381674 0.011996834797376446 2.7046466770962243 chr14 107349540 203793 0.00189840589908443 0.4757829780547382 chr15 102531392 590439 0.005758616834149682 1.2972376561229373 chr16 90354753 302333 0.0033460663657616328 0.9371442602801826 chr17 81195210 819788 0.01009650692448483 1.869723693191358 chr18 78077248 257115 0.0032930848177435764 0.7985481382739974 chr19 59128983 168403 0.002848061837965317 0.5161442733917772 chr20 63025520 477308 0.007573249693140175 2.222399079232793 chr21 48129895 366880 0.007622705181467776 2.416811678445793 chr22 51304566 148347 0.002891497025820275 0.6863812751454167 chrMT 16571 3901804 235.45977913221893 939.7080362926818 chrX 155270560 28609608 0.18425648751443932 7.624401689997234 chrY 59373566 800269 0.013478540264871408 2.601801779300628