BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818895.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,248,404 number of mapped reads = 1,231,584 (98.65%) number of supplementary alignments = 19,864 (1.59%) number of secondary alignments = 0 number of mapped bases = 113,898,786 bp number of sequenced bases = 113,823,387 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 215,011 duplication rate = 14.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1227 >>>>>>> ACTG content number of A's = 33,157,301 bp (29.13%) number of C's = 25,143,648 bp (22.09%) number of T's = 31,700,049 bp (27.85%) number of G's = 23,820,885 bp (20.93%) number of N's = 1,504 bp (0%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 706,231 number of insertions = 14,459 mapped reads with insertion percentage = 1.13% number of deletions = 38,397 mapped reads with deletion percentage = 3.04% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.4816X There is a 2.78% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 9738491 0.03907108018800082 0.7058667267294197 chr2 243199373 8843159 0.03636176726491807 0.7206345867091528 chr3 198022430 7150803 0.036111075901856166 0.23822382199158615 chr4 191154276 5497505 0.028759518829701722 0.28635827378619916 chr5 180915260 5823385 0.032188467683710045 0.23701606956347943 chr6 171115067 5677960 0.03318211598514583 0.25146905701750727 chr7 159138663 10217090 0.06420243709097895 1.0230073255092655 chr8 146364022 9875923 0.06747507252841138 0.40822083773976 chr9 141213431 4198021 0.029728199154087545 0.3724078030060094 chr10 135534747 5375586 0.03966205064742549 0.6844916030358962 chr11 135006516 5061930 0.037493968068918984 0.294340598610425 chr12 133851895 4559953 0.03406715310231506 0.23312562020098526 chr13 115169878 3481941 0.03023308750921834 0.2133629265020162 chr14 107349540 3443271 0.032075321421964176 0.24799456804405984 chr15 102531392 3177235 0.03098792416667863 0.21898130635335078 chr16 90354753 2871573 0.031781095124016334 0.49632252948163147 chr17 81195210 2882811 0.035504692949251564 0.30468694019626974 chr18 78077248 2214721 0.02836576668276013 0.4417225303764465 chr19 59128983 1692512 0.028624067489880556 0.5780567899458274 chr20 63025520 4647335 0.07373735274219079 0.3678078709930967 chr21 48129895 1134118 0.023563691547633752 0.23652086423156743 chr22 51304566 1016798 0.01981885978725558 0.19841600371324536 chrMT 16571 164777 9.943696819745337 6.960324586026658 chrX 155270560 4715131 0.030367192595943494 0.2532586144994189 chrY 59373566 436757 0.007356085029489386 0.5644944444392295