BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094151.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 525,972 number of mapped reads = 491,601 (93.47%) number of supplementary alignments = 61,096 (11.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 246,450 number of mapped paired reads (second in pair) = 245,151 number of mapped paired reads (both in pair) = 489,380 number of mapped paired reads (singletons) = 2,221 number of mapped bases = 60,316,214 bp number of sequenced bases = 60,051,468 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 526,857 duplication rate = 39.6% >>>>>>> Insert size mean insert size = 262,322.1107 std insert size = 3,513,376.0165 median insert size = 173 >>>>>>> Mapping quality mean mapping quality = 22.1344 >>>>>>> ACTG content number of A's = 18,747,903 bp (31.22%) number of C's = 12,914,216 bp (21.51%) number of T's = 15,475,748 bp (25.77%) number of G's = 12,913,022 bp (21.5%) number of N's = 579 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0147 number of mismatches = 828,531 number of insertions = 16,014 mapped reads with insertion percentage = 3.17% number of deletions = 35,979 mapped reads with deletion percentage = 7% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 28.9135X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% 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 21404720 0.08587629556999178 77.3955621303767 chr2 243199373 1070857 0.004403206253331912 1.630818879399294 chr3 198022430 11111235 0.056110992072968706 35.88077860559795 chr4 191154276 1112803 0.005821491537024262 1.7634011863217818 chr5 180915260 752769 0.0041608927848319705 2.395026194024991 chr6 171115067 1482490 0.008663702302731764 3.5116403425675937 chr7 159138663 474164 0.0029795650601890503 1.4100962591320458 chr8 146364022 1037221 0.00708658443398064 2.672622383449457 chr9 141213431 1365160 0.00966735239228059 4.148200213007723 chr10 135534747 172861 0.0012753998795600363 0.27143447954765143 chr11 135006516 753047 0.005577856701375806 1.490317257740881 chr12 133851895 585851 0.00437685996152688 1.5835204715703712 chr13 115169878 966431 0.008391352120734209 2.923148142809107 chr14 107349540 1401136 0.013052091327079744 3.451941696774285 chr15 102531392 707209 0.006897487551909955 2.5706488106323393 chr16 90354753 149842 0.0016583742971440583 0.5765947743057239 chr17 81195210 98285 0.001210477810205799 0.2145556105175263 chr18 78077248 325574 0.004169895947152236 1.8402442361700786 chr19 59128983 125169 0.002116880650560149 0.6086835846055215 chr20 63025520 1980081 0.03141713071149591 10.490148649716902 chr21 48129895 72228 0.0015006889169402926 0.44652690635282405 chr22 51304566 365768 0.007129345953340683 1.698672706709868 chrMT 16571 109489 6.6072657051475465 46.09490863779251 chrX 155270560 12632833 0.08136013034280291 72.7058163359954 chrY 59373566 58991 9.93556627540276E-4 0.33717342763604835