BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013271.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 = 1,289,439 number of mapped reads = 1,087,402 (84.33%) number of supplementary alignments = 15,332 (1.19%) number of secondary alignments = 0 number of mapped bases = 68,173,660 bp number of sequenced bases = 68,115,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 161,558 duplication rate = 11.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.446 >>>>>>> ACTG content number of A's = 18,911,448 bp (27.76%) number of C's = 11,776,574 bp (17.29%) number of T's = 22,560,798 bp (33.12%) number of G's = 14,852,887 bp (21.81%) number of N's = 13,882 bp (0.02%) GC percentage = 39.09% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 677,092 number of insertions = 5,309 mapped reads with insertion percentage = 0.49% number of deletions = 33,522 mapped reads with deletion percentage = 3.03% homopolymer indels = 42.2% >>>>>>> Coverage mean coverageData = 0.022X std coverageData = 0.2985X There is a 1.23% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 3690262 0.014805427505835583 0.37835958539427167 chr2 243199373 10999812 0.04522960673915882 0.4283520048082787 chr3 198022430 4368305 0.022059647485388398 0.23930179773260726 chr4 191154276 4694687 0.024559675557558544 0.2786380381365011 chr5 180915260 1279276 0.007071133745157816 0.1333132089728832 chr6 171115067 3305482 0.01931730535453082 0.2505242241810503 chr7 159138663 6045804 0.037990792972792536 0.47222478920298655 chr8 146364022 4883342 0.03336436053936807 0.4431129087390835 chr9 141213431 1949308 0.013803984409953186 0.212476517151569 chr10 135534747 3432822 0.025327984712289316 0.3422116711636822 chr11 135006516 1549554 0.011477623791136126 0.17240388886690186 chr12 133851895 2876388 0.02148933341586236 0.24067749568835176 chr13 115169878 907630 0.007880793274783186 0.13996357394176015 chr14 107349540 1581011 0.014727692358998463 0.20011193920307732 chr15 102531392 1974069 0.019253313170662895 0.22132538447243247 chr16 90354753 1758555 0.019462783546096353 0.2236002516315103 chr17 81195210 877296 0.010804775306326567 0.17630008131844963 chr18 78077248 1481455 0.01897422152993917 0.30041361540850964 chr19 59128983 1116550 0.018883294508887462 0.2874850331656953 chr20 63025520 1156807 0.018354580811074626 0.22002104666887662 chr21 48129895 1300864 0.027028191106587704 0.28134535924060144 chr22 51304566 510390 0.009948237355716058 0.15448907368787596 chrMT 16571 11579 0.6987508297628386 1.1476416890001955 chrX 155270560 6162735 0.039690299307222184 0.32936502166829273 chrY 59373566 259677 0.004373612998080661 0.14961287940332704