BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008671.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 = 4,554,317 number of mapped reads = 3,801,864 (83.48%) number of supplementary alignments = 38,293 (0.84%) number of secondary alignments = 0 number of mapped bases = 249,002,882 bp number of sequenced bases = 248,880,826 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 449,291 duplication rate = 8.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3974 >>>>>>> ACTG content number of A's = 69,792,484 bp (28.04%) number of C's = 46,166,297 bp (18.55%) number of T's = 78,925,183 bp (31.71%) number of G's = 53,923,340 bp (21.67%) number of N's = 73,522 bp (0.03%) GC percentage = 40.22% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,132,828 number of insertions = 22,418 mapped reads with insertion percentage = 0.58% number of deletions = 73,659 mapped reads with deletion percentage = 1.91% homopolymer indels = 47.28% >>>>>>> Coverage mean coverageData = 0.0804X std coverageData = 0.7452X There is a 4.26% of reference with a coverageData >= 1X There is a 1.89% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% 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 18974527 0.07612629779566327 0.6231821787975859 chr2 243199373 7480050 0.030756863834513256 0.6423029317210114 chr3 198022430 18284256 0.09233426738577039 0.5877894073234926 chr4 191154276 10894429 0.056992860572996025 0.4668339364352855 chr5 180915260 6269452 0.034654080589995556 0.3084632698209277 chr6 171115067 4011025 0.02344051327753622 0.27192315599935635 chr7 159138663 32257553 0.20270091750111033 0.9950268694087802 chr8 146364022 27816078 0.19004723715504346 0.8295133638368792 chr9 141213431 7076441 0.050111671035030655 0.745234468429387 chr10 135534747 14738041 0.10873994548423807 1.575033078331431 chr11 135006516 5570626 0.04126190472169506 0.6160175988113986 chr12 133851895 3719918 0.02779129873357415 0.28469529619691697 chr13 115169878 5096943 0.04425586870900393 0.3438338207830268 chr14 107349540 20367848 0.1897339103642177 0.7582616484953297 chr15 102531392 10231110 0.09978514677729139 0.5311091656282954 chr16 90354753 5818210 0.06439296004715989 0.6533296217430474 chr17 81195210 8495960 0.10463622176726928 0.5475794399290813 chr18 78077248 6918836 0.08861526471834663 1.9381770492167654 chr19 59128983 2915243 0.0493031141766805 0.5377255054781279 chr20 63025520 6191772 0.09824229930986686 0.512723374767821 chr21 48129895 2490103 0.05173713759400472 0.43801881803028386 chr22 51304566 4747729 0.09254008697783352 0.4953754832034138 chrMT 16571 107098 6.462977490797176 4.929031893426319 chrX 155270560 17762235 0.11439538184186365 0.8576177095461665 chrY 59373566 767399 0.01292492689423438 0.3499793314718806