BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818954.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,185,609 number of mapped reads = 2,136,117 (97.74%) number of supplementary alignments = 30,038 (1.37%) number of secondary alignments = 0 number of mapped bases = 197,872,649 bp number of sequenced bases = 197,764,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 934,045 duplication rate = 36.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2386 >>>>>>> ACTG content number of A's = 55,755,795 bp (28.19%) number of C's = 41,145,218 bp (20.81%) number of T's = 57,435,803 bp (29.04%) number of G's = 43,419,566 bp (21.96%) number of N's = 7,982 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,267,312 number of insertions = 27,391 mapped reads with insertion percentage = 1.26% number of deletions = 60,455 mapped reads with deletion percentage = 2.78% homopolymer indels = 42.4% >>>>>>> Coverage mean coverageData = 0.0639X std coverageData = 0.7015X There is a 2.92% of reference with a coverageData >= 1X There is a 1.43% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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% 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 23654319 0.09490174550056588 1.2621230651502402 chr2 243199373 17262728 0.07098179484204509 0.8933600487433586 chr3 198022430 13086479 0.06608584189174933 0.4806232979724945 chr4 191154276 12620754 0.06602391672368343 0.5335224328458326 chr5 180915260 9742592 0.05385168724849413 0.4410625372873686 chr6 171115067 10411536 0.060845232290386214 0.49134458715237533 chr7 159138663 10225769 0.06425697443493038 0.5976380269749453 chr8 146364022 13186125 0.09009129989609059 0.6550867954553793 chr9 141213431 7752593 0.05489982748170746 0.8041276594436546 chr10 135534747 9612747 0.07092459470928145 0.8773874563054839 chr11 135006516 7094496 0.05254928584335885 0.49434130542179755 chr12 133851895 9164562 0.06846792867594441 0.497569426983195 chr13 115169878 3389669 0.029431905797451658 0.31702944454770837 chr14 107349540 5038684 0.04693717364787963 0.4435099631064909 chr15 102531392 5681542 0.05541270716387036 0.44293624604629694 chr16 90354753 5831407 0.06453901766518028 0.6518925476452078 chr17 81195210 4253486 0.052385922765640976 0.4518349376099877 chr18 78077248 5110875 0.06545921034511872 1.0084889130568715 chr19 59128983 3100304 0.05243289910803979 1.0901674116342146 chr20 63025520 4189865 0.06647886443459729 0.511767444383702 chr21 48129895 2709088 0.05628701246906938 0.4926386245601534 chr22 51304566 2351090 0.045826135630891024 0.42991716455573886 chrMT 16571 346140 20.888298835314707 13.337505283225054 chrX 155270560 11505682 0.07410085981527986 0.6057338936821192 chrY 59373566 550117 0.009265352193937619 0.43362934668295483