BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231742.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 = 1,149,310 number of mapped reads = 869,235 (75.63%) number of supplementary alignments = 7,289 (0.63%) number of secondary alignments = 0 number of mapped bases = 56,902,833 bp number of sequenced bases = 56,867,890 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,199 duplication rate = 5.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3981 >>>>>>> ACTG content number of A's = 16,309,133 bp (28.68%) number of C's = 9,474,726 bp (16.66%) number of T's = 19,194,948 bp (33.75%) number of G's = 11,886,428 bp (20.9%) number of N's = 2,655 bp (0%) GC percentage = 37.56% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 485,305 number of insertions = 4,789 mapped reads with insertion percentage = 0.55% number of deletions = 19,753 mapped reads with deletion percentage = 2.24% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.0184X std coverageData = 0.2179X There is a 1.5% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.05% 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 2932955 0.011767092046683407 0.19495282889623147 chr2 243199373 4921291 0.020235623716020026 0.21032354046308177 chr3 198022430 4204521 0.021232549262222466 0.17282330488287062 chr4 191154276 1518039 0.007941433651214792 0.12251959305396926 chr5 180915260 3867504 0.021377433832834223 0.17464094034024513 chr6 171115067 3569015 0.020857397671474483 0.19089410285697367 chr7 159138663 4809573 0.03022252989520215 0.3247195892072972 chr8 146364022 2173105 0.014847262122927996 0.49185953999437876 chr9 141213431 3280704 0.023232237732400966 0.21279965173170892 chr10 135534747 3457548 0.025510417634822456 0.24196528795914155 chr11 135006516 2285529 0.01692902733672499 0.16469592698689303 chr12 133851895 3825018 0.028576494938678306 0.2053497746835431 chr13 115169878 2831956 0.024589380914339425 0.188813221740431 chr14 107349540 1790531 0.01667944734555919 0.15692076032230537 chr15 102531392 853119 0.008320563910806945 0.10722711422138602 chr16 90354753 1268660 0.014040877296183854 0.15004369555900363 chr17 81195210 888914 0.010947862564799082 0.1237789762036758 chr18 78077248 812829 0.010410574409589847 0.26658223909285117 chr19 59128983 475629 0.008043923231353396 0.14346380662495273 chr20 63025520 1283969 0.020372207956396077 0.16900470872379864 chr21 48129895 504517 0.010482403919642875 0.1347129893451303 chr22 51304566 277901 0.005416691372070081 0.08561355352541006 chrMT 16571 107012 6.457787701406071 5.322209327067881 chrX 155270560 4798330 0.03090302501646159 0.22093607989384437 chrY 59373566 164664 0.0027733554019645714 0.08700878326991991