BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080670.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 = 1,603,166 number of mapped reads = 1,449,998 (90.45%) number of supplementary alignments = 12,383 (0.77%) number of secondary alignments = 0 number of mapped bases = 95,894,215 bp number of sequenced bases = 95,858,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,124 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0467 >>>>>>> ACTG content number of A's = 25,764,813 bp (26.88%) number of C's = 17,886,432 bp (18.66%) number of T's = 30,035,067 bp (31.33%) number of G's = 22,167,626 bp (23.13%) number of N's = 4,135 bp (0%) GC percentage = 41.78% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 650,740 number of insertions = 7,318 mapped reads with insertion percentage = 0.5% number of deletions = 22,499 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.76% >>>>>>> Coverage mean coverageData = 0.031X std coverageData = 0.2606X There is a 2.71% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 11510765 0.04618148975444278 0.3206704959596409 chr2 243199373 6578352 0.02704921447309817 0.37793584423187543 chr3 198022430 6002339 0.030311409672126536 0.19285737812740153 chr4 191154276 3982380 0.02083332940980091 0.16371277211679905 chr5 180915260 4359856 0.024098884748583398 0.17226340259010992 chr6 171115067 5818442 0.034003095706352966 0.25382211541491373 chr7 159138663 5882010 0.03696153963540588 0.5333802114036732 chr8 146364022 11312943 0.0772931957281141 0.3432210239802454 chr9 141213431 2934731 0.020782237066387828 0.19184912855030134 chr10 135534747 4481491 0.03306525521459084 0.21245014650312022 chr11 135006516 4099538 0.030365482507525784 0.21137743478845933 chr12 133851895 3095998 0.02313002740827838 0.17012271418345104 chr13 115169878 1884392 0.016361847669926332 0.1420771754360861 chr14 107349540 1889670 0.017602963179907432 0.15036322083490825 chr15 102531392 1812390 0.01767644001166004 0.16024840139356206 chr16 90354753 2362175 0.026143339686845252 0.1813430396211471 chr17 81195210 1586143 0.019534933156771194 0.15915280180831617 chr18 78077248 3028761 0.038791851372630345 0.2669111857952779 chr19 59128983 1669315 0.028231755651877185 0.22144845414872472 chr20 63025520 2571311 0.04079793391629295 0.22665544979687866 chr21 48129895 1407301 0.029239644092304794 0.1920870070483387 chr22 51304566 968973 0.018886681547993212 0.15101004830666587 chrMT 16571 117860 7.112425321344517 4.175695640950124 chrX 155270560 6348934 0.0408894899329274 0.22989328343293727 chrY 59373566 188145 0.003168834427091679 0.0670553662926213