BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695924.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 162,038,866 number of mapped reads = 160,605,890 (99.12%) number of supplementary alignments = 1,395,278 (0.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 80,764,543 number of mapped paired reads (second in pair) = 79,841,347 number of mapped paired reads (both in pair) = 159,557,492 number of mapped paired reads (singletons) = 1,048,398 number of mapped bases = 15,956,160,090 bp number of sequenced bases = 15,953,008,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,453,351 duplication rate = 7.91% >>>>>>> Insert size mean insert size = 39,842.1355 std insert size = 1,912,265.3777 median insert size = 310 >>>>>>> Mapping quality mean mapping quality = 54.4849 >>>>>>> ACTG content number of A's = 4,829,065,582 bp (30.27%) number of C's = 3,131,011,872 bp (19.63%) number of T's = 4,824,081,047 bp (30.24%) number of G's = 3,166,156,024 bp (19.85%) number of N's = 2,693,800 bp (0.02%) GC percentage = 39.47% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 70,435,404 number of insertions = 1,079,819 mapped reads with insertion percentage = 0.66% number of deletions = 1,440,595 mapped reads with deletion percentage = 0.88% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 5.1543X std coverageData = 7.2235X There is a 78.68% of reference with a coverageData >= 1X There is a 67.1% of reference with a coverageData >= 2X There is a 56.76% of reference with a coverageData >= 3X There is a 47.73% of reference with a coverageData >= 4X There is a 39.98% of reference with a coverageData >= 5X There is a 33.42% of reference with a coverageData >= 6X There is a 27.92% of reference with a coverageData >= 7X There is a 23.34% of reference with a coverageData >= 8X There is a 19.54% of reference with a coverageData >= 9X There is a 16.38% of reference with a coverageData >= 10X There is a 13.78% of reference with a coverageData >= 11X There is a 11.62% of reference with a coverageData >= 12X There is a 9.83% of reference with a coverageData >= 13X There is a 8.34% of reference with a coverageData >= 14X There is a 7.1% of reference with a coverageData >= 15X There is a 6.07% of reference with a coverageData >= 16X There is a 5.21% of reference with a coverageData >= 17X There is a 4.49% of reference with a coverageData >= 18X There is a 3.88% of reference with a coverageData >= 19X There is a 3.36% of reference with a coverageData >= 20X There is a 2.93% of reference with a coverageData >= 21X There is a 2.56% of reference with a coverageData >= 22X There is a 2.24% of reference with a coverageData >= 23X There is a 1.97% of reference with a coverageData >= 24X There is a 1.74% of reference with a coverageData >= 25X There is a 1.54% of reference with a coverageData >= 26X There is a 1.37% of reference with a coverageData >= 27X There is a 1.22% of reference with a coverageData >= 28X There is a 1.09% of reference with a coverageData >= 29X There is a 0.98% of reference with a coverageData >= 30X There is a 0.88% of reference with a coverageData >= 31X There is a 0.79% of reference with a coverageData >= 32X There is a 0.72% of reference with a coverageData >= 33X There is a 0.65% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.54% of reference with a coverageData >= 36X There is a 0.49% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.41% of reference with a coverageData >= 39X There is a 0.38% of reference with a coverageData >= 40X There is a 0.35% of reference with a coverageData >= 41X There is a 0.32% of reference with a coverageData >= 42X There is a 0.3% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1250058579 5.015267661058305 8.065614422125206 chr2 243199373 1495507593 6.149306943320121 8.942153721766214 chr3 198022430 1221005727 6.165997089319629 6.940583619542263 chr4 191154276 1184890478 6.198608280151682 6.691608390318417 chr5 180915260 1065754021 5.890901745933427 6.7695215182798165 chr6 171115067 1067804848 6.2402736750236025 7.842534574981244 chr7 159138663 858636968 5.395527094506255 6.5902822174665365 chr8 146364022 950747860 6.495775717341247 8.203466829555301 chr9 141213431 643866516 4.559527457413028 6.8952652713819775 chr10 135534747 727849483 5.370205789368537 7.270968737531804 chr11 135006516 731930293 5.421444199034068 6.685925470515224 chr12 133851895 788408000 5.890151947419198 7.4406502424053125 chr13 115169878 541568317 4.702343411356223 6.444737982360076 chr14 107349540 540520722 5.035147071892436 7.083762678170507 chr15 102531392 426214253 4.156914723248856 6.1257662954087 chr16 90354753 406138878 4.4949365087634074 7.659742567440899 chr17 81195210 293490943 3.614633708072188 6.246269872142854 chr18 78077248 442230637 5.664014144043602 7.223879616353684 chr19 59128983 135027210 2.2836044719389137 5.807123240474955 chr20 63025520 282478161 4.481964781885179 6.440971348471468 chr21 48129895 193506857 4.020512760312483 8.402607986003504 chr22 51304566 107174149 2.088978766529279 4.798294676724155 chrMT 16571 727761 43.91774787278981 19.281764876820773 chrX 155270560 511305865 3.292999426291758 5.036500534479095 chrY 59373566 89315971 1.504305316611773 4.1322984393490625