BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714263.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 392,918 number of mapped reads = 90,051 (22.92%) number of supplementary alignments = 3,123 (0.79%) number of secondary alignments = 0 number of mapped bases = 10,611,487 bp number of sequenced bases = 10,441,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,667 duplication rate = 36.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0022 >>>>>>> ACTG content number of A's = 2,713,431 bp (25.99%) number of C's = 1,842,281 bp (17.64%) number of T's = 2,526,396 bp (24.2%) number of G's = 3,359,017 bp (32.17%) number of N's = 162 bp (0%) GC percentage = 49.81% >>>>>>> Mismatches and indels general error rate = 0.0375 number of mismatches = 356,256 number of insertions = 10,596 mapped reads with insertion percentage = 10.98% number of deletions = 28,841 mapped reads with deletion percentage = 30.54% homopolymer indels = 28.7% >>>>>>> Coverage mean coverageData = 0.0034X std coverageData = 1.7727X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% 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 0.01% 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% 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 575262 0.0023079661655085707 0.28648930795847066 chr2 243199373 2217791 0.009119229924988334 6.151891274276323 chr3 198022430 587207 0.0029653559952779085 0.32908393079175097 chr4 191154276 496720 0.002598529367975007 0.4826645273572435 chr5 180915260 661740 0.0036577345658956573 1.0231284579943076 chr6 171115067 438142 0.002560510933850144 0.3247388195422394 chr7 159138663 386720 0.002430081997107139 0.34089600285430344 chr8 146364022 447209 0.0030554571669258995 0.37826850346060875 chr9 141213431 354965 0.0025136773286104776 0.2879068438175714 chr10 135534747 442250 0.003263000889358653 0.34562166880923634 chr11 135006516 402505 0.002981374617503647 0.30531748702679945 chr12 133851895 383128 0.0028623277989452446 0.4425410364076078 chr13 115169878 323417 0.002808173505228511 0.3245039031533536 chr14 107349540 285061 0.0026554468701030297 0.3385498498526638 chr15 102531392 243995 0.002379710206216648 0.33520229808724744 chr16 90354753 169245 0.0018731167357626444 0.2354016416533104 chr17 81195210 173715 0.002139473498498249 0.28426021289828285 chr18 78077248 217797 0.002789506617856203 0.29226988379604424 chr19 59128983 71756 0.0012135503835741602 0.18935816837642097 chr20 63025520 133124 0.0021122237468250956 0.19185290294033674 chr21 48129895 81824 0.0017000660400360316 0.1901537144115097 chr22 51304566 55000 0.0010720293394548938 0.15532734235626902 chrMT 16571 1828 0.11031319775511436 0.8739399764296509 chrX 155270560 1416858 0.009125091066844868 0.6318556322831076 chrY 59373566 44228 7.449106223466517E-4 0.11256754289231595