BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008731.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 = 1,582,048 number of mapped reads = 1,276,408 (80.68%) number of supplementary alignments = 10,438 (0.66%) number of secondary alignments = 0 number of mapped bases = 83,334,535 bp number of sequenced bases = 83,293,961 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,778 duplication rate = 5.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0902 >>>>>>> ACTG content number of A's = 22,272,091 bp (26.74%) number of C's = 15,248,796 bp (18.31%) number of T's = 26,425,311 bp (31.73%) number of G's = 19,276,266 bp (23.14%) number of N's = 71,497 bp (0.09%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 747,227 number of insertions = 6,986 mapped reads with insertion percentage = 0.54% number of deletions = 24,244 mapped reads with deletion percentage = 1.88% homopolymer indels = 47.65% >>>>>>> Coverage mean coverageData = 0.0269X std coverageData = 0.2826X There is a 2.05% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.11% 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% 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 5864194 0.023527299456557824 0.34485678731980807 chr2 243199373 8487153 0.03489792303041834 0.3783963883978895 chr3 198022430 4077223 0.020589702893758045 0.17811918908037586 chr4 191154276 4344565 0.02272805553143891 0.201546490101157 chr5 180915260 3227913 0.017842126750391315 0.1686512921916867 chr6 171115067 5338697 0.03119945597777196 0.2526857732818804 chr7 159138663 2732938 0.01717331255950039 0.24766919171151516 chr8 146364022 5450880 0.03724193914266718 0.37568064606781293 chr9 141213431 2840984 0.02011836961882188 0.30476611633469425 chr10 135534747 4725796 0.03486778191278138 0.3040452795971532 chr11 135006516 2527065 0.018718096539873677 0.25052165867456005 chr12 133851895 4632074 0.03460596504816013 0.23924056145738617 chr13 115169878 2369941 0.020577785104539226 0.17907037468274367 chr14 107349540 2567256 0.023914923156633926 0.20791379014619743 chr15 102531392 3521328 0.03434390123173203 0.23644596305406695 chr16 90354753 2312660 0.02559533309775082 0.22651290276816044 chr17 81195210 3132496 0.03857981277466983 0.30182772973467736 chr18 78077248 3005850 0.03849841121449363 0.6364624354796541 chr19 59128983 1836358 0.031056816925127902 0.27584574125023154 chr20 63025520 2285389 0.03626132715763392 0.24546115212030747 chr21 48129895 1452791 0.03018479471023155 0.23065631931092076 chr22 51304566 1090468 0.021254794358849072 0.17820721480947863 chrMT 16571 48520 2.928006758795486 3.1676404576322508 chrX 155270560 5186461 0.03340273262362163 0.24173565987276352 chrY 59373566 275535 0.004640701553954162 0.10599629672863281