BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063563.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 = 1,208,946 number of mapped reads = 116,294 (9.62%) number of supplementary alignments = 1,022 (0.08%) number of secondary alignments = 0 number of mapped bases = 7,207,726 bp number of sequenced bases = 7,203,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,499 duplication rate = 8.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3015 >>>>>>> ACTG content number of A's = 1,965,691 bp (27.29%) number of C's = 1,345,242 bp (18.68%) number of T's = 2,255,352 bp (31.31%) number of G's = 1,636,982 bp (22.73%) number of N's = 120 bp (0%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 60,283 number of insertions = 1,078 mapped reads with insertion percentage = 0.86% number of deletions = 2,394 mapped reads with deletion percentage = 1.87% homopolymer indels = 47.24% >>>>>>> Coverage mean coverageData = 0.0023X std coverageData = 0.1163X There is a 0.13% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 557895 0.002238289308013399 0.09924889703297599 chr2 243199373 661994 0.0027220218203440846 0.22618130432094732 chr3 198022430 478542 0.0024166050280263703 0.08437644157202502 chr4 191154276 439461 0.0022989859771695613 0.09119917397869377 chr5 180915260 413480 0.0022854899028418056 0.19147029686842737 chr6 171115067 392485 0.0022936904790505676 0.10820068612201744 chr7 159138663 406772 0.002556085317871497 0.08655976232810113 chr8 146364022 342082 0.002337200053166071 0.08950960346682367 chr9 141213431 307837 0.0021799413683249434 0.07754563934019379 chr10 135534747 358780 0.0026471440567192705 0.09560987802167596 chr11 135006516 359600 0.002663575141810192 0.09385132177257519 chr12 133851895 304273 0.0022732065167997808 0.07931660206436394 chr13 115169878 223374 0.0019395175533658202 0.0901330013143305 chr14 107349540 204625 0.0019061562816198375 0.11719539521007802 chr15 102531392 234172 0.002283905401381852 0.12936061636583832 chr16 90354753 208820 0.002311112510041392 0.07760700077378481 chr17 81195210 186854 0.002301293389105096 0.08926495835457393 chr18 78077248 201305 0.0025782799106853767 0.086167080935985 chr19 59128983 146076 0.002470463596507317 0.08559467095407641 chr20 63025520 109073 0.0017306164233155078 0.06376215593302577 chr21 48129895 109846 0.002282282145016107 0.08517155146966805 chr22 51304566 78306 0.001526296899188271 0.06493441207806147 chrMT 16571 1036 0.06251885824633396 0.34120681495434274 chrX 155270560 458839 0.0029550933544646198 0.09871465722366901 chrY 59373566 22199 3.738869246964213E-4 0.05104968814420908