BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080990.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 = 3,232,312 number of mapped reads = 2,879,201 (89.08%) number of supplementary alignments = 20,290 (0.63%) number of secondary alignments = 0 number of mapped bases = 189,141,325 bp number of sequenced bases = 189,077,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,303 duplication rate = 2.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1618 >>>>>>> ACTG content number of A's = 52,892,739 bp (27.97%) number of C's = 37,274,239 bp (19.71%) number of T's = 56,738,668 bp (30.01%) number of G's = 42,169,449 bp (22.3%) number of N's = 2,536 bp (0%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,457,278 number of insertions = 13,895 mapped reads with insertion percentage = 0.48% number of deletions = 36,680 mapped reads with deletion percentage = 1.26% homopolymer indels = 45.79% >>>>>>> Coverage mean coverageData = 0.0611X std coverageData = 0.5766X There is a 5.11% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% 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 14785895 0.05932139683615874 1.03328666513349 chr2 243199373 16281165 0.06694575236425465 0.6418523418718232 chr3 198022430 12779603 0.06453613865863579 0.2910415436937419 chr4 191154276 12492974 0.06535545142605129 0.33656831729845055 chr5 180915260 11597906 0.0641068420651746 0.295344510289334 chr6 171115067 11331104 0.06621920675167664 0.4800376432492899 chr7 159138663 10442189 0.06561692050912857 0.9672885812016193 chr8 146364022 10011114 0.06839873531215206 0.5616790737273241 chr9 141213431 8138749 0.057634383233702464 0.5763374502064281 chr10 135534747 9105508 0.06718209316464065 0.5111021672835577 chr11 135006516 8628005 0.06390806351894897 0.5538677170908027 chr12 133851895 8528965 0.06371941913859344 0.3030132648613029 chr13 115169878 6340242 0.055051217471985166 0.2681533806278759 chr14 107349540 5718826 0.0532729436940298 0.3271944803271025 chr15 102531392 5319362 0.051880325588479284 0.2815110134274579 chr16 90354753 5223392 0.05780981992170351 0.34739035859394435 chr17 81195210 4532119 0.05581756608548706 0.3574573371304936 chr18 78077248 5316631 0.06809449790033584 1.2131426398702938 chr19 59128983 3179696 0.05377559089761446 0.7569051769565134 chr20 63025520 3630304 0.057600540225610196 0.3062413552161032 chr21 48129895 2545739 0.05289309274412504 0.31359160972670286 chr22 51304566 1930738 0.03763286877819023 0.22360100020641738 chrMT 16571 49548 2.9900428459356707 2.2605761298362617 chrX 155270560 10736743 0.0691486074372373 0.3953999138317203 chrY 59373566 494808 0.00833380969571543 0.19870366193434852