BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975231.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 3,464,408 number of mapped reads = 3,200,547 (92.38%) number of supplementary alignments = 157,820 (4.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,599,758 number of mapped paired reads (second in pair) = 1,600,789 number of mapped paired reads (both in pair) = 3,191,496 number of mapped paired reads (singletons) = 9,051 number of mapped bases = 303,208,289 bp number of sequenced bases = 303,068,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 379,719 duplication rate = 8.57% >>>>>>> Insert size mean insert size = 314,071.8256 std insert size = 5,467,586.8788 median insert size = 126 >>>>>>> Mapping quality mean mapping quality = 51.0866 >>>>>>> ACTG content number of A's = 83,877,947 bp (27.68%) number of C's = 66,863,212 bp (22.06%) number of T's = 85,236,375 bp (28.12%) number of G's = 67,087,102 bp (22.14%) number of N's = 4,074 bp (0%) GC percentage = 44.2% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,194,070 number of insertions = 62,966 mapped reads with insertion percentage = 1.91% number of deletions = 57,652 mapped reads with deletion percentage = 1.74% homopolymer indels = 36.78% >>>>>>> Coverage mean coverageData = 0.0979X std coverageData = 1.9468X There is a 6.02% of reference with a coverageData >= 1X There is a 2.78% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 28893048 0.11591966304469108 4.537486735470097 chr2 243199373 26081790 0.10724447879230346 1.1865249663929882 chr3 198022430 18124018 0.09152507622495087 0.7605376532962853 chr4 191154276 17879473 0.09353425606864268 1.3080580818437009 chr5 180915260 17299593 0.09562263017503332 0.4184621605378205 chr6 171115067 16345891 0.09552572597245337 0.5424490830166646 chr7 159138663 17094646 0.10741981664128974 1.352130160360648 chr8 146364022 15139173 0.10343507094933481 0.8175341130983734 chr9 141213431 11972816 0.08478524964102034 1.3448016368333908 chr10 135534747 17191658 0.1268431777129447 5.219779359764867 chr11 135006516 14014239 0.1038041674966266 0.8499874639427915 chr12 133851895 13900679 0.10385119314149419 0.44586372011931064 chr13 115169878 6766324 0.058750813298595314 0.31665192786030405 chr14 107349540 9139576 0.0851384738118114 0.40810907199992474 chr15 102531392 6841333 0.06672427699021194 0.33637693723354883 chr16 90354753 11058710 0.12239212252619405 1.669092403412939 chr17 81195210 11097903 0.13668174514235507 1.092778213533265 chr18 78077248 8316815 0.10652033995870347 1.8691636970726673 chr19 59128983 9452873 0.15986868909955715 2.3770007209654733 chr20 63025520 5636329 0.08942931371292137 0.5654491183705487 chr21 48129895 4531967 0.09416116532147016 0.8734399088257598 chr22 51304566 3635945 0.0708698130298968 0.618819212902609 chrMT 16571 162185 9.787278981352966 4.903688864602963 chrX 155270560 8443177 0.054377191658225486 0.5292881498317461 chrY 59373566 4188128 0.07053859625005511 1.612004774914073