BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818806.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 = 3,575,976 number of mapped reads = 3,485,125 (97.46%) number of supplementary alignments = 24,350 (0.68%) number of secondary alignments = 0 number of mapped bases = 237,045,786 bp number of sequenced bases = 236,948,082 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,774,103 duplication rate = 42.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6001 >>>>>>> ACTG content number of A's = 68,717,171 bp (29%) number of C's = 49,965,644 bp (21.09%) number of T's = 68,597,063 bp (28.95%) number of G's = 49,653,406 bp (20.96%) number of N's = 14,798 bp (0.01%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,190,372 number of insertions = 30,811 mapped reads with insertion percentage = 0.88% number of deletions = 58,832 mapped reads with deletion percentage = 1.67% homopolymer indels = 39.05% >>>>>>> Coverage mean coverageData = 0.0766X std coverageData = 0.921X There is a 3.13% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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% 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 19445989 0.07801781565069801 1.453652713545728 chr2 243199373 21048508 0.08654836457987085 1.5963920485409242 chr3 198022430 15963959 0.08061692304250584 0.5773610089202139 chr4 191154276 15527595 0.08123069661282388 0.731564404265781 chr5 180915260 14616846 0.08079388106896013 0.6187510131647137 chr6 171115067 14022824 0.0819496742504855 0.68591299482445 chr7 159138663 12896668 0.08104044458385326 0.760744000876329 chr8 146364022 12310443 0.08410839516284951 0.7042080688707156 chr9 141213431 10175977 0.07206097131086632 0.717103967582546 chr10 135534747 11446159 0.08445184171111486 0.9996153793315006 chr11 135006516 11261712 0.08341606267359718 0.6842985899892186 chr12 133851895 10885786 0.08132709663916227 0.6345051878097488 chr13 115169878 7660575 0.06651543904561573 0.5277732659728064 chr14 107349540 7284511 0.06785786879012244 0.6472730170222678 chr15 102531392 6857614 0.0668830673829143 0.5328087831712605 chr16 90354753 7211778 0.07981625493459099 1.0851825537119193 chr17 81195210 6440949 0.07932671151413981 0.6367787625663278 chr18 78077248 6430604 0.08236207300749125 0.9364060999258956 chr19 59128983 4805443 0.08127051669398745 1.1763336945241258 chr20 63025520 5005143 0.07941454509221027 0.6145613749472267 chr21 48129895 3144889 0.06534169667313838 0.5591478241492133 chr22 51304566 2868790 0.0559168554315419 0.5548709822543749 chrMT 16571 175939 10.617283205600145 9.80180792808569 chrX 155270560 7307238 0.04706132315102103 0.5320623756350116 chrY 59373566 2249847 0.03789307517759671 1.7084255591705542