BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124887.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 = 5,715,428 number of mapped reads = 5,505,268 (96.32%) number of supplementary alignments = 6,744 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,767,767 number of mapped paired reads (second in pair) = 2,737,501 number of mapped paired reads (both in pair) = 5,418,766 number of mapped paired reads (singletons) = 86,502 number of mapped bases = 364,486,101 bp number of sequenced bases = 364,331,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 273,247 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 58,145.0933 std insert size = 2,325,455.6047 median insert size = 201 >>>>>>> Mapping quality mean mapping quality = 51.83 >>>>>>> ACTG content number of A's = 102,213,478 bp (28.06%) number of C's = 68,824,679 bp (18.89%) number of T's = 106,820,001 bp (29.32%) number of G's = 86,470,270 bp (23.73%) number of N's = 3,233 bp (0%) GC percentage = 42.62% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 2,478,535 number of insertions = 41,708 mapped reads with insertion percentage = 0.75% number of deletions = 101,147 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.98% >>>>>>> Coverage mean coverageData = 0.1177X std coverageData = 0.8636X There is a 8.77% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 33502043 0.13441107133690952 1.0913705342397169 chr2 243199373 29940108 0.12310931410172674 1.0492095501709513 chr3 198022430 21645366 0.10930764762355456 0.3993789757974935 chr4 191154276 15369905 0.08040576084209594 0.522759513913444 chr5 180915260 18479328 0.1021435560493902 0.391574165212615 chr6 171115067 19943221 0.11654859709110245 0.6860849705951759 chr7 159138663 18782199 0.11802410957794712 1.1451084656687802 chr8 146364022 23493734 0.16051577210689114 0.5860641017419078 chr9 141213431 14325303 0.10144433782647772 0.819553943039297 chr10 135534747 16624304 0.12265713677098611 1.7470715968307815 chr11 135006516 24356771 0.18041181804884143 0.7251685017237491 chr12 133851895 11877002 0.08873241577939557 0.36005087130148594 chr13 115169878 21344007 0.18532629686383795 0.951073338491436 chr14 107349540 5816295 0.05418090287112549 0.3289412038357138 chr15 102531392 7963590 0.0776697735655437 0.33696368374754376 chr16 90354753 10774727 0.11924914453587185 1.2847711596725666 chr17 81195210 8952181 0.11025503844377027 1.1083915525135908 chr18 78077248 9699068 0.12422399928849952 1.3106885784430136 chr19 59128983 6561405 0.11096766200088373 0.8003960651095847 chr20 63025520 9889464 0.15691205721111068 0.5156488099472523 chr21 48129895 3091606 0.06423463005684928 0.36233988739157436 chr22 51304566 3008465 0.05863932266769394 0.30106539802294485 chrMT 16571 329728 19.897893911049422 12.622658687725227 chrX 155270560 27896628 0.1796646318529411 0.7129049919805065 chrY 59373566 819653 0.013805015518185314 0.6844457565158762