BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081173.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 = 2,524,115 number of mapped reads = 2,291,722 (90.79%) number of supplementary alignments = 20,305 (0.8%) number of secondary alignments = 0 number of mapped bases = 153,813,028 bp number of sequenced bases = 153,747,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,690 duplication rate = 2.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8545 >>>>>>> ACTG content number of A's = 44,147,162 bp (28.71%) number of C's = 28,768,056 bp (18.71%) number of T's = 47,386,884 bp (30.82%) number of G's = 33,400,203 bp (21.72%) number of N's = 44,903 bp (0.03%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,347,154 number of insertions = 12,819 mapped reads with insertion percentage = 0.55% number of deletions = 40,442 mapped reads with deletion percentage = 1.75% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0497X std coverageData = 0.4802X There is a 4.39% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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% of reference with a coverageData >= 7X There is a 0% 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 12207943 0.048978586095478574 0.9225628901585908 chr2 243199373 13113752 0.05392181664876249 0.5207559896017038 chr3 198022430 10419881 0.05261970070764206 0.250319092525316 chr4 191154276 10420115 0.05451154542836384 0.2687108732469857 chr5 180915260 9571551 0.05290626672399001 0.2550179866694055 chr6 171115067 9286618 0.054271188170706204 0.38661761263455013 chr7 159138663 8752841 0.05500134810105826 0.7813993502854565 chr8 146364022 7899317 0.05397034661974512 0.6012660741662083 chr9 141213431 6496988 0.04600828656305362 0.4224821907129074 chr10 135534747 6932095 0.05114625698161373 0.3747769096204438 chr11 135006516 6918060 0.051242415588296494 0.4270112849268517 chr12 133851895 6911084 0.051632320932027145 0.25618393050261273 chr13 115169878 5049560 0.04384445036921894 0.2288420386489006 chr14 107349540 4723669 0.04400269437577469 0.26856862495975437 chr15 102531392 4285743 0.04179932522519542 0.2333071892528997 chr16 90354753 4079389 0.04514858227768051 0.2796940105041633 chr17 81195210 3823953 0.04709579542931166 0.29756703547042357 chr18 78077248 4257869 0.0545340558109835 0.8988791549810189 chr19 59128983 2771459 0.046871413296589254 0.612529270897227 chr20 63025520 2991754 0.04746893004611465 0.2537613739869145 chr21 48129895 2041600 0.042418542571098485 0.2476598528577609 chr22 51304566 1516672 0.029562125133267867 0.18517424224684378 chrMT 16571 10898 0.6576549393518798 0.9298356188085419 chrX 155270560 8966041 0.05774462976110861 0.31643474016090756 chrY 59373566 364176 0.006133638663374202 0.12514039925307535