BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081118.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,689,121 number of mapped reads = 2,502,429 (93.06%) number of supplementary alignments = 15,895 (0.59%) number of secondary alignments = 0 number of mapped bases = 171,806,617 bp number of sequenced bases = 171,739,395 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 109,222 duplication rate = 3.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0578 >>>>>>> ACTG content number of A's = 49,012,915 bp (28.54%) number of C's = 32,350,524 bp (18.84%) number of T's = 53,805,431 bp (31.33%) number of G's = 36,568,553 bp (21.29%) number of N's = 1,972 bp (0%) GC percentage = 40.13% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,460,314 number of insertions = 12,982 mapped reads with insertion percentage = 0.51% number of deletions = 37,151 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0555X std coverageData = 0.4146X There is a 4.47% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 14683265 0.0589096425962365 0.5795521007308272 chr2 243199373 11510876 0.04733102663056619 0.4252761565569866 chr3 198022430 15195165 0.07673456486722237 0.3322824349294552 chr4 191154276 10406245 0.054438986235390306 0.3098140899918064 chr5 180915260 9861559 0.05450927135720889 0.2799888646191834 chr6 171115067 14461443 0.08451297278222729 0.5103765129339227 chr7 159138663 8474144 0.053250064065198284 0.46274413312268436 chr8 146364022 12374977 0.08454930952908632 0.49446045159392393 chr9 141213431 8632525 0.06113104779672126 0.5029756849523564 chr10 135534747 7532143 0.05557352019847722 0.3981308354458737 chr11 135006516 7554943 0.05595983974580901 0.3668866294998414 chr12 133851895 8261475 0.0617210163516923 0.3105962004032802 chr13 115169878 4536910 0.039393199669795605 0.2341782701390673 chr14 107349540 5081690 0.04733779017590574 0.3243213461538547 chr15 102531392 4163197 0.040604120540955885 0.2428610839004075 chr16 90354753 3926607 0.043457669570520545 0.3102267177074581 chr17 81195210 3615070 0.04452319293219391 0.2580984423894437 chr18 78077248 4259075 0.05454950205212151 0.9458967432455812 chr19 59128983 3416469 0.05777993847788655 0.452758153526277 chr20 63025520 2629175 0.04171603820166815 0.2624772325539323 chr21 48129895 4130925 0.08582867259527577 0.41047513234523997 chr22 51304566 1537055 0.02995941920646985 0.20234077502079767 chrMT 16571 24113 1.4551324603222497 1.5696450517018175 chrX 155270560 5116608 0.0329528533934572 0.2516216487307359 chrY 59373566 420963 0.0070900743943862156 0.1956139091563195