BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082984.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 = 4,348,945 number of mapped reads = 3,714,486 (85.41%) number of supplementary alignments = 25,399 (0.58%) number of secondary alignments = 0 number of mapped bases = 253,098,256 bp number of sequenced bases = 252,999,213 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,933 duplication rate = 3.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5874 >>>>>>> ACTG content number of A's = 71,894,739 bp (28.42%) number of C's = 46,347,820 bp (18.32%) number of T's = 81,655,227 bp (32.27%) number of G's = 53,075,983 bp (20.98%) number of N's = 25,444 bp (0.01%) GC percentage = 39.3% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,233,406 number of insertions = 21,039 mapped reads with insertion percentage = 0.56% number of deletions = 57,372 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.96% >>>>>>> Coverage mean coverageData = 0.0818X std coverageData = 0.6582X There is a 6.31% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 25774635 0.10340850865924221 1.1932337861816895 chr2 243199373 27238228 0.11199958151207898 0.798382643885393 chr3 198022430 19901941 0.10050346821822154 0.44137207246637833 chr4 191154276 14754831 0.077188077132002 0.41729651456305883 chr5 180915260 14639314 0.08091807180886787 0.36717890482970783 chr6 171115067 18569288 0.10851930414754184 0.6500688201231923 chr7 159138663 13231208 0.08314263643147486 0.7744384169365249 chr8 146364022 14201279 0.09702711640433057 0.8165499803346168 chr9 141213431 8127730 0.05755635241239907 0.6618934059446941 chr10 135534747 9650308 0.07120172659487829 0.6720342000770053 chr11 135006516 8370531 0.06200094075459291 0.43966901434097305 chr12 133851895 8647473 0.06460478575966369 0.3233910241957533 chr13 115169878 6310478 0.05479278184179374 0.3068814842299694 chr14 107349540 5523526 0.051453653178206445 0.3383526830675111 chr15 102531392 4991183 0.048679559524560045 0.26863132175427185 chr16 90354753 9376285 0.10377190671972729 0.49126260378932063 chr17 81195210 6106382 0.07520618519245162 0.404273599149199 chr18 78077248 8901295 0.11400625954439378 1.390788635674729 chr19 59128983 4156967 0.07030337389702779 0.7988712596208756 chr20 63025520 4867449 0.07722981103527587 0.36780183919781007 chr21 48129895 5274822 0.10959554347666871 0.42624687297387587 chr22 51304566 3258137 0.06350579010842816 0.30632165633504643 chrMT 16571 139266 8.404200108623499 5.8444379979165415 chrX 155270560 10633634 0.06848454723161944 0.4033392894032459 chrY 59373566 452066 0.007613927046254894 0.15886764583367283