BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084889.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 = 2,566,248 number of mapped reads = 2,285,911 (89.08%) number of supplementary alignments = 17,498 (0.68%) number of secondary alignments = 0 number of mapped bases = 158,242,020 bp number of sequenced bases = 158,180,734 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,244 duplication rate = 3.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6824 >>>>>>> ACTG content number of A's = 46,060,277 bp (29.12%) number of C's = 29,010,146 bp (18.34%) number of T's = 50,684,706 bp (32.04%) number of G's = 32,400,877 bp (20.48%) number of N's = 24,728 bp (0.02%) GC percentage = 38.82% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,309,406 number of insertions = 12,861 mapped reads with insertion percentage = 0.56% number of deletions = 34,362 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.0511X std coverageData = 0.4171X There is a 4.25% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 13203481 0.05297271054742929 0.8580274561647643 chr2 243199373 13729471 0.056453562485130254 0.4088578069620117 chr3 198022430 10348419 0.05225882239703856 0.2630813813743489 chr4 191154276 9196261 0.04810910429228379 0.26205249661045693 chr5 180915260 8252695 0.0456163565196214 0.2593885914043686 chr6 171115067 9130406 0.05335828200330249 0.2751218307162062 chr7 159138663 8672636 0.054497353669485084 0.37676731704138594 chr8 146364022 10970610 0.07495428077263414 0.7358457166549123 chr9 141213431 9250452 0.06550688510641739 0.39543018418642123 chr10 135534747 6652801 0.049085575081347955 0.3578924783144655 chr11 135006516 6262484 0.04638653144711919 0.30847256783087085 chr12 133851895 7196417 0.05376402777114213 0.2699260063883498 chr13 115169878 6167484 0.05355118983455032 0.26601094997705405 chr14 107349540 3319598 0.030923262456457663 0.21798873588487203 chr15 102531392 4818698 0.04699729425306154 0.2493815621649459 chr16 90354753 3376990 0.037374790897829135 0.23806735766061307 chr17 81195210 3949452 0.04864144079435228 0.26319230897335255 chr18 78077248 4819660 0.06172937857645802 0.628470256938575 chr19 59128983 3332630 0.056362038224131134 0.47778088079250686 chr20 63025520 2581480 0.040959281256227636 0.2400736058680294 chr21 48129895 1788760 0.037165258723294535 0.23805268185258438 chr22 51304566 1495340 0.029146333681099652 0.19473590114932315 chrMT 16571 60473 3.6493271377708045 2.5079130233387144 chrX 155270560 9319275 0.0600195877441287 0.2996486849771103 chrY 59373566 346047 0.005828300762665999 0.12027085817308657