BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238244.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 = 874,858 number of mapped reads = 280,765 (32.09%) number of supplementary alignments = 2,729 (0.31%) number of secondary alignments = 0 number of mapped bases = 17,199,549 bp number of sequenced bases = 17,192,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,514 duplication rate = 8.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7 >>>>>>> ACTG content number of A's = 4,771,300 bp (27.75%) number of C's = 3,446,079 bp (20.04%) number of T's = 5,145,779 bp (29.93%) number of G's = 3,825,527 bp (22.25%) number of N's = 3,508 bp (0.02%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 181,924 number of insertions = 1,530 mapped reads with insertion percentage = 0.54% number of deletions = 4,577 mapped reads with deletion percentage = 1.61% homopolymer indels = 44.8% >>>>>>> Coverage mean coverageData = 0.0056X std coverageData = 0.2349X There is a 0.33% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.05% 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% 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 1427740 0.005728130161810108 0.23874827220984693 chr2 243199373 1540567 0.006334584587929838 0.348819667864497 chr3 198022430 1083088 0.005469521811241282 0.1444232147543127 chr4 191154276 1080988 0.005655055291569832 0.1826019256087608 chr5 180915260 1039868 0.005747818066867328 0.16615241843831802 chr6 171115067 972109 0.005681025154845073 0.22050799603366225 chr7 159138663 917213 0.0057636088095072155 0.17146732630125608 chr8 146364022 859339 0.00587124477899357 0.16681195815002675 chr9 141213431 687306 0.0048671432676966825 0.1409610942174148 chr10 135534747 810388 0.005979189971114935 0.15022231139188222 chr11 135006516 702147 0.005200837861781427 0.12378016503290991 chr12 133851895 820620 0.006130805992698124 0.16737800619669724 chr13 115169878 575698 0.004998685506986471 0.21270538651355916 chr14 107349540 580185 0.005404634244357265 0.46362436540464647 chr15 102531392 541837 0.005284596155682739 0.6010253717670347 chr16 90354753 525807 0.005819361821508161 0.14356145895283334 chr17 81195210 414498 0.005104956314541215 0.14399023508189962 chr18 78077248 448865 0.00574898592737285 0.13943854146585144 chr19 59128983 333776 0.0056448797707209005 0.13318250268209947 chr20 63025520 345040 0.005474607746195509 0.1260105850308822 chr21 48129895 223040 0.004634126045776747 0.11493238156803576 chr22 51304566 208738 0.004068604731984284 0.10571610202289994 chrMT 16571 3892 0.23486814314163298 1.4336301964403277 chrX 155270560 1013327 0.006526201747452962 0.23888140142827333 chrY 59373566 43473 7.321945257591568E-4 0.057808247283956754