BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714108.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 = 849,174 number of mapped reads = 213,899 (25.19%) number of supplementary alignments = 4,602 (0.54%) number of secondary alignments = 0 number of mapped bases = 26,105,704 bp number of sequenced bases = 25,990,388 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 204,964 duplication rate = 38.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 31.6172 >>>>>>> ACTG content number of A's = 5,772,350 bp (22.21%) number of C's = 4,620,159 bp (17.78%) number of T's = 5,750,270 bp (22.12%) number of G's = 9,846,926 bp (37.89%) number of N's = 683 bp (0%) GC percentage = 55.66% >>>>>>> Mismatches and indels general error rate = 0.0354 number of mismatches = 659,485 number of insertions = 52,443 mapped reads with insertion percentage = 23.1% number of deletions = 40,950 mapped reads with deletion percentage = 18.5% homopolymer indels = 41.47% >>>>>>> Coverage mean coverageData = 0.0084X std coverageData = 15.2941X There is a 0.01% 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% of reference with a coverageData >= 4X There is a 0% 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 362909 0.0014560003844483903 0.964836025775502 chr2 243199373 5242974 0.02155833683008714 21.995954381660166 chr3 198022430 200172 0.0010108551844354198 0.34434156716503733 chr4 191154276 83902 4.3892295665936344E-4 0.08149638395799132 chr5 180915260 424776 0.0023479279746772054 0.9520417531096831 chr6 171115067 1994121 0.011653684476539989 11.253493238259981 chr7 159138663 500197 0.0031431519567309673 2.448278568831701 chr8 146364022 177745 0.0012144036326085655 0.4743719760143816 chr9 141213431 52536 3.720326007800207E-4 0.07646721100103239 chr10 135534747 8073661 0.05956893843613402 52.483932198684236 chr11 135006516 76015 5.630468976771461E-4 0.0994319587590246 chr12 133851895 93854 7.011779698748382E-4 0.13663491156107221 chr13 115169878 206743 0.0017951134757649043 0.789638705110426 chr14 107349540 125408 0.0011682211213946516 0.3624134630070764 chr15 102531392 136714 0.001333386754370798 0.72657802416434 chr16 90354753 181807 0.002012146499919047 1.050663774518405 chr17 81195210 63290 7.794794791466147E-4 0.1507909336248498 chr18 78077248 71486 9.155804261953496E-4 0.2611931177543165 chr19 59128983 21322 3.6060150062110826E-4 0.07419663852054162 chr20 63025520 51797 8.218416920637862E-4 0.2221495335561668 chr21 48129895 34864 7.243730741569247E-4 0.20066988425577642 chr22 51304566 13004 2.5346671873220796E-4 0.05652617878940703 chrMT 16571 7288568 439.83875445054616 3530.5449172742146 chrX 155270560 620962 0.003999225609800081 0.4843365164192303 chrY 59373566 6877 1.158259552744398E-4 0.021577716403763245