BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927025.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 27,383,484 number of mapped reads = 26,998,342 (98.59%) number of supplementary alignments = 242,591 (0.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,534,154 number of mapped paired reads (second in pair) = 13,464,188 number of mapped paired reads (both in pair) = 26,766,526 number of mapped paired reads (singletons) = 231,816 number of mapped bases = 2,552,546,046 bp number of sequenced bases = 2,550,626,566 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,780,223 duplication rate = 4.9% >>>>>>> Insert size mean insert size = 95,524.7264 std insert size = 3,012,659.9143 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.5238 >>>>>>> ACTG content number of A's = 735,383,790 bp (28.83%) number of C's = 504,695,247 bp (19.79%) number of T's = 744,996,251 bp (29.21%) number of G's = 564,995,824 bp (22.15%) number of N's = 555,454 bp (0.02%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 23,478,649 number of insertions = 413,110 mapped reads with insertion percentage = 1.51% number of deletions = 1,351,479 mapped reads with deletion percentage = 4.87% homopolymer indels = 53.1% >>>>>>> Coverage mean coverageData = 0.8245X std coverageData = 3.9923X There is a 33.7% of reference with a coverageData >= 1X There is a 18.51% of reference with a coverageData >= 2X There is a 10.62% of reference with a coverageData >= 3X There is a 6.43% of reference with a coverageData >= 4X There is a 4% of reference with a coverageData >= 5X There is a 2.55% of reference with a coverageData >= 6X There is a 1.66% of reference with a coverageData >= 7X There is a 1.09% of reference with a coverageData >= 8X There is a 0.73% of reference with a coverageData >= 9X There is a 0.49% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 203518445 0.8165213157081763 5.793391398803877 chr2 243199373 221408611 0.9103995963015908 5.855585040257205 chr3 198022430 174167201 0.8795326923318737 1.769525000602318 chr4 191154276 157521853 0.824056130452452 2.5818352483441007 chr5 180915260 154126451 0.8519262056722026 1.668964954337699 chr6 171115067 147289397 0.8607622904416711 1.7592130882563384 chr7 159138663 131733749 0.8277922317344089 2.5954269570821418 chr8 146364022 132198155 0.9032148282998126 2.0584902295241494 chr9 141213431 108448809 0.7679780048683896 3.966864598300073 chr10 135534747 127414339 0.9400861537004972 10.758713007205179 chr11 135006516 123300473 0.9132927554400412 4.135621814295062 chr12 133851895 111280236 0.8313684016203132 1.6691035979864437 chr13 115169878 78987247 0.6858325142968372 1.499279420354973 chr14 107349540 78070829 0.7272581605845726 1.6058981847747669 chr15 102531392 76550510 0.7466055859263083 1.6341555879242167 chr16 90354753 80224381 0.8878822456633798 5.1124924195625985 chr17 81195210 65089887 0.8016468828641492 2.1369265021821793 chr18 78077248 68466611 0.8769086097911648 4.239096940892032 chr19 59128983 40956303 0.6926603658987336 3.496654798731718 chr20 63025520 58146065 0.922579694701448 1.9147006239504407 chr21 48129895 33701095 0.7002112720171112 2.415063223973071 chr22 51304566 31489409 0.613774006001727 1.5594343296293909 chrMT 16571 136431 8.233118097881842 6.9124500774922115 chrX 155270560 143822184 0.9262682120808993 2.1783581633869273 chrY 59373566 4497375 0.07574709256978097 2.360134699311978