BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124890.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 1,817,770 number of mapped reads = 1,783,986 (98.14%) number of supplementary alignments = 14,277 (0.79%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 892,876 number of mapped paired reads (second in pair) = 891,110 number of mapped paired reads (both in pair) = 1,778,040 number of mapped paired reads (singletons) = 5,946 number of mapped bases = 241,235,617 bp number of sequenced bases = 241,088,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,186 duplication rate = 14.8% >>>>>>> Insert size mean insert size = 61,555.3367 std insert size = 2,424,422.1215 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.6788 >>>>>>> ACTG content number of A's = 70,040,368 bp (29.05%) number of C's = 48,886,104 bp (20.28%) number of T's = 70,777,583 bp (29.36%) number of G's = 51,359,789 bp (21.3%) number of N's = 24,620 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 2,840,101 number of insertions = 37,040 mapped reads with insertion percentage = 2% number of deletions = 83,426 mapped reads with deletion percentage = 4.54% homopolymer indels = 49.33% >>>>>>> Coverage mean coverageData = 0.0779X std coverageData = 0.9393X There is a 4.53% of reference with a coverageData >= 1X There is a 2.39% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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% 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 20139818 0.08080147571628317 1.1258007664632537 chr2 243199373 21150749 0.08696876451239864 0.8572329661505369 chr3 198022430 14986451 0.07568057315527336 0.3868994350453145 chr4 191154276 10844164 0.05672990542989475 0.4756583436216254 chr5 180915260 12838236 0.07096270375423279 0.36844707638990376 chr6 171115067 14655300 0.08564587711028393 0.6647602158042646 chr7 159138663 15956325 0.10026680317152092 1.4276087855985422 chr8 146364022 14176316 0.09685656219531874 0.4904967578427346 chr9 141213431 9396355 0.06654009419259843 1.1040141009979327 chr10 135534747 11037918 0.08143976540569335 2.554010416593965 chr11 135006516 16289969 0.12066061315144226 0.9011115531764855 chr12 133851895 7748352 0.057887503198964796 0.3292665407030258 chr13 115169878 10960450 0.09516767917388955 0.4736801793828336 chr14 107349540 3922075 0.03653555478672754 0.2706958398617161 chr15 102531392 5098522 0.04972644865681722 0.30483144620830627 chr16 90354753 7460910 0.08257351995638791 1.3626338160339326 chr17 81195210 5414837 0.06668911873003346 1.0306274002861715 chr18 78077248 5267605 0.06746658130163605 1.1556636942525087 chr19 59128983 3577047 0.06049566250784323 0.6683969905597594 chr20 63025520 6941592 0.11013938480793177 0.4806226028513447 chr21 48129895 2067418 0.042954965931257486 0.33221322758525496 chr22 51304566 1718891 0.03350366515136294 0.2511053900945655 chrMT 16571 119802 7.22961800736226 4.977613400559993 chrX 155270560 18988598 0.12229361444951316 0.5945294569728753 chrY 59373566 477917 0.00804932282490831 0.4980165629255693