BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003997.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,718,076 number of mapped reads = 2,987,642 (80.35%) number of supplementary alignments = 20,413 (0.55%) number of secondary alignments = 0 number of mapped bases = 198,742,419 bp number of sequenced bases = 198,650,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,305 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5362 >>>>>>> ACTG content number of A's = 54,925,772 bp (27.65%) number of C's = 36,216,735 bp (18.23%) number of T's = 63,056,800 bp (31.74%) number of G's = 44,430,337 bp (22.37%) number of N's = 20,899 bp (0.01%) GC percentage = 40.6% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 2,018,105 number of insertions = 18,936 mapped reads with insertion percentage = 0.63% number of deletions = 54,582 mapped reads with deletion percentage = 1.81% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 0.0642X std coverageData = 0.6557X There is a 5.33% of reference with a coverageData >= 1X There is a 0.74% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 16123484 0.06468783883190406 1.2048227409480399 chr2 243199373 16358572 0.06726403854667833 0.7710011904371551 chr3 198022430 14166480 0.07153977455988193 0.3141358952962443 chr4 191154276 13630322 0.07130534710089352 0.3338405033625813 chr5 180915260 10799000 0.05969092933343489 0.2890605982304271 chr6 171115067 12087533 0.07063979351391657 0.39557459222560754 chr7 159138663 12673636 0.07963894983835575 1.0106445406926714 chr8 146364022 13147961 0.08983055275701565 0.9343281465898581 chr9 141213431 7760984 0.054959248175196596 0.6660089363544996 chr10 135534747 8652901 0.0638426764466532 0.5896941460635289 chr11 135006516 8846915 0.06552954081120055 0.502563157022343 chr12 133851895 8392593 0.06270059157548723 0.31033791324918086 chr13 115169878 6490359 0.05635465724813914 0.2722909888809029 chr14 107349540 4468850 0.041628962732397363 0.3601469991119061 chr15 102531392 5418185 0.05284415723137749 0.2737270786572541 chr16 90354753 5288334 0.05852856462349026 0.40412035042629485 chr17 81195210 3915499 0.04822327573264482 0.29673420955871826 chr18 78077248 5860061 0.07505465612722416 1.4014492124753926 chr19 59128983 2928189 0.049522059258147566 0.8610093557265164 chr20 63025520 4460551 0.0707737278486556 0.3422529111601907 chr21 48129895 2511651 0.05218484270534976 0.32953200024031937 chr22 51304566 2220837 0.04328731676630887 0.23678088292419108 chrMT 16571 122353 7.383561643835616 5.196769501374247 chrX 155270560 11898102 0.07662819017333357 0.4101844741676453 chrY 59373566 519067 0.00874239219520687 0.18886767595400258