BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238525.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 = 3,258,765 number of mapped reads = 2,840,784 (87.17%) number of supplementary alignments = 21,837 (0.67%) number of secondary alignments = 0 number of mapped bases = 175,531,095 bp number of sequenced bases = 175,442,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 647,506 duplication rate = 17.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.793 >>>>>>> ACTG content number of A's = 42,886,952 bp (24.45%) number of C's = 31,594,070 bp (18.01%) number of T's = 57,982,696 bp (33.05%) number of G's = 42,966,687 bp (24.49%) number of N's = 11,923 bp (0.01%) GC percentage = 42.5% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,065,229 number of insertions = 10,967 mapped reads with insertion percentage = 0.38% number of deletions = 51,603 mapped reads with deletion percentage = 1.8% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.7591X There is a 3.22% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% 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% 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 25059295 0.10053854589995184 0.962839268492498 chr2 243199373 5080120 0.020888705169482488 1.7084421128543916 chr3 198022430 9865307 0.04981913917529444 0.3683430335211207 chr4 191154276 2022948 0.01058280276189061 0.17108233382301213 chr5 180915260 10243722 0.05662165811772871 0.38558871763110314 chr6 171115067 20451109 0.11951670509529123 0.9651558621372522 chr7 159138663 13907992 0.0873954307382864 1.002786347660229 chr8 146364022 8763486 0.05987459131179109 0.5345063963100931 chr9 141213431 4938608 0.034972650724703375 0.43748777102444125 chr10 135534747 4307008 0.03177788792419408 0.42861608264824613 chr11 135006516 9720025 0.07199671014397557 0.5280335227807954 chr12 133851895 2634426 0.019681648885135322 0.23818088207450777 chr13 115169878 1658778 0.0144028805865367 0.36313062388521317 chr14 107349540 4412423 0.04110332470916969 0.3426356392340153 chr15 102531392 2872459 0.028015410148727913 0.38139238664108144 chr16 90354753 5502046 0.06089381927700029 0.45168781505830496 chr17 81195210 6856779 0.08444807273729571 0.5092585322417599 chr18 78077248 10594239 0.13568919591018372 1.3306269267696174 chr19 59128983 2356667 0.03985637635607567 0.6438228769858002 chr20 63025520 5803207 0.09207709829288199 0.5180484476134498 chr21 48129895 4231094 0.08790989467149264 0.4989493760523043 chr22 51304566 1705547 0.03324357134216865 0.2956188170461564 chrMT 16571 127967 7.722346267575886 5.61457718874224 chrX 155270560 11915886 0.0767427257298486 0.4931631114258407 chrY 59373566 499957 0.00842053179019094 0.25435933318147286