BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094059.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 = 399,850 number of mapped reads = 379,148 (94.82%) number of supplementary alignments = 8,169 (2.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,418 number of mapped paired reads (second in pair) = 188,730 number of mapped paired reads (both in pair) = 376,668 number of mapped paired reads (singletons) = 2,480 number of mapped bases = 51,305,053 bp number of sequenced bases = 50,089,243 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 362,225 duplication rate = 50.57% >>>>>>> Insert size mean insert size = 295,490.4538 std insert size = 4,994,525.754 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 41.704 >>>>>>> ACTG content number of A's = 13,675,026 bp (27.3%) number of C's = 11,312,282 bp (22.58%) number of T's = 13,389,387 bp (26.73%) number of G's = 11,712,008 bp (23.38%) number of N's = 540 bp (0%) GC percentage = 45.97% >>>>>>> Mismatches and indels general error rate = 0.0438 number of mismatches = 2,098,762 number of insertions = 43,781 mapped reads with insertion percentage = 11.27% number of deletions = 167,004 mapped reads with deletion percentage = 41.23% homopolymer indels = 33.13% >>>>>>> Coverage mean coverageData = 0.0166X std coverageData = 6.4567X There is a 0.01% 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% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% 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 491977 0.001973824570731962 0.7863698293456242 chr2 243199373 2244402 0.00922865043735125 3.7724700093140875 chr3 198022430 2206226 0.011141293438324134 6.389034834296951 chr4 191154276 881355 0.004610699893524747 2.154176129813782 chr5 180915260 466523 0.0025786824173925408 1.1194843934029628 chr6 171115067 1794612 0.010487749743276552 5.545653018354433 chr7 159138663 1306245 0.00820821901714733 2.7979139181697974 chr8 146364022 597394 0.00408156315901185 2.435962089192653 chr9 141213431 1357229 0.00961118917930689 5.6889902445605 chr10 135534747 668809 0.004934594373795525 2.849872794408492 chr11 135006516 1998708 0.014804529879135612 4.814776242316171 chr12 133851895 1016759 0.007596149460566098 3.524040456918277 chr13 115169878 1307392 0.01135185712361352 4.10731344880556 chr14 107349540 242100 0.002255249533440013 0.9258915008637802 chr15 102531392 916227 0.008936063210767684 3.4505000666384134 chr16 90354753 254972 0.0028218991423727318 0.6497008301762 chr17 81195210 1580150 0.01946112338400258 5.073593188798334 chr18 78077248 283536 0.003631480453819274 1.3515303990223575 chr19 59128983 619683 0.010480190400027681 4.122503150480125 chr20 63025520 464236 0.007365841646368011 2.1028938474660723 chr21 48129895 115024 0.002389866007395196 0.46294887883172414 chr22 51304566 84866 0.0016541607622214366 0.46442896770317676 chrMT 16571 7445856 449.3305171685475 1885.9819115418732 chrX 155270560 22749916 0.14651789753318337 13.702923070178935 chrY 59373566 210856 0.003551344717950746 1.4998460557551516