BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094058.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 = 432,402 number of mapped reads = 409,130 (94.62%) number of supplementary alignments = 11,924 (2.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 205,444 number of mapped paired reads (second in pair) = 203,686 number of mapped paired reads (both in pair) = 406,216 number of mapped paired reads (singletons) = 2,914 number of mapped bases = 54,216,046 bp number of sequenced bases = 52,950,893 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 392,056 duplication rate = 50.34% >>>>>>> Insert size mean insert size = 278,044.9419 std insert size = 4,823,025.5095 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 41.9085 >>>>>>> ACTG content number of A's = 14,569,731 bp (27.52%) number of C's = 11,989,029 bp (22.64%) number of T's = 14,095,487 bp (26.62%) number of G's = 12,296,073 bp (23.22%) number of N's = 573 bp (0%) GC percentage = 45.86% >>>>>>> Mismatches and indels general error rate = 0.043 number of mismatches = 2,196,214 number of insertions = 44,728 mapped reads with insertion percentage = 10.71% number of deletions = 179,760 mapped reads with deletion percentage = 40.34% homopolymer indels = 31.11% >>>>>>> Coverage mean coverageData = 0.0175X std coverageData = 5.8863X 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% 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 1598288 0.006412373191238709 2.7524752154298824 chr2 243199373 3645787 0.014990939141936027 5.126767849983881 chr3 198022430 2422008 0.012230978076574457 3.4680600621357542 chr4 191154276 644033 0.0033691791440752287 1.4101119392754866 chr5 180915260 286960 0.0015861569665267595 0.5822932292731092 chr6 171115067 1724630 0.010078773484043927 4.336439778221806 chr7 159138663 1142249 0.007177696346487465 2.9380995405472956 chr8 146364022 1260362 0.008611146255600983 2.439502645673102 chr9 141213431 1556874 0.011024971130401896 4.492779026367004 chr10 135534747 752685 0.005553446748234975 2.609661718871407 chr11 135006516 1496389 0.011083827983532291 3.69891345480285 chr12 133851895 1535411 0.011470969462180569 4.81203830120611 chr13 115169878 1758263 0.015266691521545243 4.53184705568539 chr14 107349540 317087 0.0029537807055344625 0.9782560771742131 chr15 102531392 646665 0.006306995227373876 1.847653267600199 chr16 90354753 320015 0.0035417616602858733 1.2601687462404965 chr17 81195210 1307294 0.01610062958147408 4.411336337928331 chr18 78077248 89997 0.001152666139052442 0.3244450851653615 chr19 59128983 195917 0.0033133835567576058 1.001340587414134 chr20 63025520 154532 0.002451895676544993 0.5071971368468514 chr21 48129895 790909 0.016432801276628592 6.255437534081033 chr22 51304566 263064 0.005127496839170222 1.4440272393282207 chrMT 16571 5580926 336.7887272946714 1415.6099214837984 chrX 155270560 24413177 0.1572299153168508 16.018260393681487 chrY 59373566 312524 0.005263689231669191 2.702188313285845