BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818898.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 = 952,366 number of mapped reads = 937,890 (98.48%) number of supplementary alignments = 13,706 (1.44%) number of secondary alignments = 0 number of mapped bases = 86,849,433 bp number of sequenced bases = 86,790,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,073 duplication rate = 12.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2366 >>>>>>> ACTG content number of A's = 25,124,050 bp (28.95%) number of C's = 18,920,282 bp (21.8%) number of T's = 24,146,998 bp (27.82%) number of G's = 18,598,250 bp (21.43%) number of N's = 1,099 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 535,044 number of insertions = 13,772 mapped reads with insertion percentage = 1.42% number of deletions = 29,031 mapped reads with deletion percentage = 3.01% homopolymer indels = 39.67% >>>>>>> Coverage mean coverageData = 0.0281X std coverageData = 0.3846X There is a 2.19% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 7491170 0.030054769652910915 0.5175523743878983 chr2 243199373 6617221 0.02720903807593287 0.6277257939951529 chr3 198022430 5320873 0.026870052044104295 0.19989387209760628 chr4 191154276 4314790 0.022572291294179578 0.23088589727288727 chr5 180915260 3864897 0.021363023771460737 0.19145107623295995 chr6 171115067 4279867 0.02501163150057382 0.21189917255217833 chr7 159138663 7797639 0.04899902294642252 0.7857528471671087 chr8 146364022 7487136 0.05115421056139056 0.3194505753248456 chr9 141213431 3439215 0.02435473011062241 0.29894613275451604 chr10 135534747 4462993 0.032928773608143454 0.49807596881162824 chr11 135006516 3810834 0.02822703757498638 0.24045078421568408 chr12 133851895 3414917 0.025512653369606758 0.19544423145502995 chr13 115169878 2595916 0.022539886688080022 0.18140623122856553 chr14 107349540 2550503 0.023758862869836236 0.2096336723348141 chr15 102531392 2437464 0.023772855829363948 0.18728347673741141 chr16 90354753 2248800 0.02488856341624884 0.45444320225181073 chr17 81195210 2208626 0.027201432202712452 0.25073029046108897 chr18 78077248 1663774 0.02130933200924295 0.33528125934575165 chr19 59128983 1605907 0.02715938814641882 0.4822177768979261 chr20 63025520 3681245 0.058408800117793556 0.31643380913421554 chr21 48129895 846026 0.017577973107982054 0.18456022062803032 chr22 51304566 809744 0.015783078644501153 0.1684649289264349 chrMT 16571 47789 2.883893548971094 2.5381139489349733 chrX 155270560 3506273 0.022581698681321174 0.20824764223718972 chrY 59373566 345814 0.005824376457361513 0.5102550750731774