BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094070.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 = 381,528 number of mapped reads = 362,164 (94.92%) number of supplementary alignments = 12,194 (3.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 181,779 number of mapped paired reads (second in pair) = 180,385 number of mapped paired reads (both in pair) = 359,820 number of mapped paired reads (singletons) = 2,344 number of mapped bases = 47,669,615 bp number of sequenced bases = 46,606,829 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 344,430 duplication rate = 49.6% >>>>>>> Insert size mean insert size = 391,630.6329 std insert size = 5,598,639.1345 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 38.0197 >>>>>>> ACTG content number of A's = 12,281,679 bp (26.35%) number of C's = 10,950,183 bp (23.49%) number of T's = 11,833,912 bp (25.39%) number of G's = 11,540,620 bp (24.76%) number of N's = 435 bp (0%) GC percentage = 48.26% >>>>>>> Mismatches and indels general error rate = 0.0411 number of mismatches = 1,840,388 number of insertions = 31,808 mapped reads with insertion percentage = 8.64% number of deletions = 150,415 mapped reads with deletion percentage = 39.63% homopolymer indels = 27.2% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 4.2618X 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 0.01% 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% 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 270555 0.001085473724857841 0.49117365138266017 chr2 243199373 1979567 0.008139687925922408 3.101656632828116 chr3 198022430 932522 0.004709173602202538 1.9042385893180764 chr4 191154276 584276 0.0030565677746073544 1.2287686184492836 chr5 180915260 326415 0.0018042424945247848 0.941588484895465 chr6 171115067 1176169 0.006873556026483629 3.71273685669358 chr7 159138663 1953218 0.012273686124911079 4.4966442452133535 chr8 146364022 662594 0.004527027823818616 1.2707475081836621 chr9 141213431 779627 0.005520912525664786 2.456371710334627 chr10 135534747 712469 0.005256725790029327 1.7776685742595402 chr11 135006516 1055432 0.007817637483512278 2.3346004514225367 chr12 133851895 1294364 0.0096701208451326 3.041681019203003 chr13 115169878 816162 0.007086592555042908 2.238013229463177 chr14 107349540 306101 0.0028514421207580395 1.2826705963987564 chr15 102531392 552608 0.005389646909309492 1.6332695721771293 chr16 90354753 271172 0.003001192422052219 1.122965037704021 chr17 81195210 952109 0.011726172024187142 3.518283862184969 chr18 78077248 82566 0.0010574911656722327 0.4115811963219696 chr19 59128983 273033 0.004617583224795191 1.1148348751625123 chr20 63025520 328148 0.005206589330798064 1.9131186834870153 chr21 48129895 551021 0.011448622524524518 4.542623770506536 chr22 51304566 89281 0.0017402154810158613 0.466453961873384 chrMT 16571 1220859 73.67443123529057 340.5493595221505 chrX 155270560 29948057 0.19287659553749276 15.6018681070049 chrY 59373566 551290 0.009285108460556336 2.299345205229456