BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237254.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 = 2,429,569 number of mapped reads = 2,167,165 (89.2%) number of supplementary alignments = 20,835 (0.86%) number of secondary alignments = 0 number of mapped bases = 131,645,466 bp number of sequenced bases = 131,566,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 636,939 duplication rate = 20.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.041 >>>>>>> ACTG content number of A's = 32,994,640 bp (25.08%) number of C's = 22,976,624 bp (17.46%) number of T's = 43,754,451 bp (33.26%) number of G's = 31,827,811 bp (24.19%) number of N's = 13,390 bp (0.01%) GC percentage = 41.66% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 920,470 number of insertions = 10,442 mapped reads with insertion percentage = 0.48% number of deletions = 44,002 mapped reads with deletion percentage = 2% homopolymer indels = 41.58% >>>>>>> Coverage mean coverageData = 0.0425X std coverageData = 0.665X There is a 1.93% of reference with a coverageData >= 1X There is a 0.92% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 10149076 0.040718357929387064 0.6709754038943904 chr2 243199373 11792559 0.04848926563638797 1.1384706736675587 chr3 198022430 12802871 0.06465364049921012 0.48175850076251064 chr4 191154276 5804185 0.030363877395031436 0.5110238750442525 chr5 180915260 6877691 0.0380160910693769 0.3696534217562119 chr6 171115067 9759874 0.05703690604872334 0.6459134777529043 chr7 159138663 9861051 0.06196514922335372 1.0147452244752257 chr8 146364022 9791310 0.06689697280934245 0.6641411688316867 chr9 141213431 5949331 0.042130064809486854 0.4506401194553462 chr10 135534747 7996684 0.059000988137750385 0.7799705516505993 chr11 135006516 5505376 0.04077859471612467 0.44669762220079917 chr12 133851895 3836984 0.02866589225352394 0.33805991214663417 chr13 115169878 4001371 0.03474320776826732 0.4146704281399798 chr14 107349540 3256571 0.03033614303330969 0.3455975092319404 chr15 102531392 2289363 0.022328410405273735 0.3076000001648437 chr16 90354753 2380117 0.026341912527833484 0.37125513320928294 chr17 81195210 2465204 0.030361446198611964 0.3677122642359415 chr18 78077248 3618482 0.04634489678734578 1.7225955777074293 chr19 59128983 2090143 0.03534887451049175 0.47321948641448514 chr20 63025520 1985913 0.031509664656475665 0.36862286464346683 chr21 48129895 1716511 0.03566413348709778 0.45469973569983174 chr22 51304566 1151101 0.022436618994106684 0.2800303176571911 chrMT 16571 9844 0.59404984611671 1.2351477064018495 chrX 155270560 6038724 0.038891622468547805 0.389534262169725 chrY 59373566 515130 0.008676083225319497 0.4201181087952481