BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085058.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 = 1,403,947 number of mapped reads = 1,000,018 (71.23%) number of supplementary alignments = 4,264 (0.3%) number of secondary alignments = 0 number of mapped bases = 63,337,331 bp number of sequenced bases = 63,315,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,700 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6317 >>>>>>> ACTG content number of A's = 18,952,529 bp (29.93%) number of C's = 11,591,566 bp (18.31%) number of T's = 18,747,373 bp (29.61%) number of G's = 14,022,320 bp (22.15%) number of N's = 1,271 bp (0%) GC percentage = 40.45% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 599,483 number of insertions = 4,710 mapped reads with insertion percentage = 0.47% number of deletions = 13,966 mapped reads with deletion percentage = 1.38% homopolymer indels = 46.71% >>>>>>> Coverage mean coverageData = 0.0205X std coverageData = 0.1782X There is a 1.91% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4981618 0.019986381498323328 0.23509801477761402 chr2 243199373 5492916 0.02258606151916354 0.1923879508678283 chr3 198022430 4382624 0.022131957475726362 0.15634981860674424 chr4 191154276 4340649 0.022707569460805575 0.16225369462576744 chr5 180915260 3684807 0.020367585354601928 0.14997944549524292 chr6 171115067 3697893 0.021610563376046832 0.16934982298067208 chr7 159138663 3537041 0.022226157574291045 0.1778831762838872 chr8 146364022 3356825 0.022934768764416708 0.24856524187876228 chr9 141213431 2547887 0.018042809256578436 0.16485995847949844 chr10 135534747 2909429 0.021466296019278363 0.18653795064653142 chr11 135006516 2917621 0.021610964318196316 0.1801939758163778 chr12 133851895 2875821 0.02148509739066451 0.15419834086055323 chr13 115169878 2128014 0.018477175082185986 0.14242226094981186 chr14 107349540 1938272 0.018055708482775053 0.14458394440175845 chr15 102531392 1787374 0.017432456198390442 0.13886831076382264 chr16 90354753 1699407 0.018808163860511023 0.1497523171138153 chr17 81195210 1565486 0.019280521597271564 0.1534796370500573 chr18 78077248 1768732 0.0226536160700746 0.2717599780916034 chr19 59128983 1075416 0.018187628899350425 0.19371365215089334 chr20 63025520 1282203 0.020344187560848367 0.15055328035822807 chr21 48129895 860727 0.01788341736461299 0.14700025641067377 chr22 51304566 660753 0.01287902912968799 0.11917461231841064 chrMT 16571 9512 0.5740148452115141 0.8710979219514884 chrX 155270560 3680367 0.023702928616989596 0.16980680538015222 chrY 59373566 155937 0.00262637079942276 0.06555611024622034