BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153308.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 359,585,682 number of mapped reads = 350,634,981 (97.51%) number of supplementary alignments = 2,346,630 (0.65%) number of secondary alignments = 0 number of mapped bases = 34,785,371,771 bp number of sequenced bases = 34,781,173,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,819,167 duplication rate = 64.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.4355 >>>>>>> ACTG content number of A's = 7,704,826,094 bp (22.15%) number of C's = 9,690,251,305 bp (27.86%) number of T's = 7,796,565,847 bp (22.42%) number of G's = 9,584,057,270 bp (27.56%) number of N's = 5,472,577 bp (0.02%) GC percentage = 55.42% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 129,582,594 number of insertions = 1,432,256 mapped reads with insertion percentage = 0.4% number of deletions = 1,566,303 mapped reads with deletion percentage = 0.44% homopolymer indels = 40.75% >>>>>>> Coverage mean coverageData = 11.2367X std coverageData = 145.7144X There is a 18.58% of reference with a coverageData >= 1X There is a 12.57% of reference with a coverageData >= 2X There is a 9.24% of reference with a coverageData >= 3X There is a 7.84% of reference with a coverageData >= 4X There is a 6.88% of reference with a coverageData >= 5X There is a 6.35% of reference with a coverageData >= 6X There is a 5.94% of reference with a coverageData >= 7X There is a 5.65% of reference with a coverageData >= 8X There is a 5.41% of reference with a coverageData >= 9X There is a 5.21% of reference with a coverageData >= 10X There is a 5.05% of reference with a coverageData >= 11X There is a 4.9% of reference with a coverageData >= 12X There is a 4.77% of reference with a coverageData >= 13X There is a 4.66% of reference with a coverageData >= 14X There is a 4.55% of reference with a coverageData >= 15X There is a 4.46% of reference with a coverageData >= 16X There is a 4.37% of reference with a coverageData >= 17X There is a 4.28% of reference with a coverageData >= 18X There is a 4.21% of reference with a coverageData >= 19X There is a 4.13% of reference with a coverageData >= 20X There is a 4.07% of reference with a coverageData >= 21X There is a 4% of reference with a coverageData >= 22X There is a 3.94% of reference with a coverageData >= 23X There is a 3.88% of reference with a coverageData >= 24X There is a 3.82% of reference with a coverageData >= 25X There is a 3.77% of reference with a coverageData >= 26X There is a 3.72% of reference with a coverageData >= 27X There is a 3.67% of reference with a coverageData >= 28X There is a 3.62% of reference with a coverageData >= 29X There is a 3.58% of reference with a coverageData >= 30X There is a 3.53% of reference with a coverageData >= 31X There is a 3.49% of reference with a coverageData >= 32X There is a 3.45% of reference with a coverageData >= 33X There is a 3.41% of reference with a coverageData >= 34X There is a 3.37% of reference with a coverageData >= 35X There is a 3.33% of reference with a coverageData >= 36X There is a 3.29% of reference with a coverageData >= 37X There is a 3.26% of reference with a coverageData >= 38X There is a 3.22% of reference with a coverageData >= 39X There is a 3.19% of reference with a coverageData >= 40X There is a 3.16% of reference with a coverageData >= 41X There is a 3.12% of reference with a coverageData >= 42X There is a 3.09% of reference with a coverageData >= 43X There is a 3.06% of reference with a coverageData >= 44X There is a 3.03% of reference with a coverageData >= 45X There is a 3% of reference with a coverageData >= 46X There is a 2.98% of reference with a coverageData >= 47X There is a 2.95% of reference with a coverageData >= 48X There is a 2.92% of reference with a coverageData >= 49X There is a 2.89% of reference with a coverageData >= 50X There is a 2.87% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3249265928 13.036139749477295 129.03989213592797 chr2 243199373 1539873194 6.331731759851206 67.16888425534162 chr3 198022430 1546272969 7.80857486194872 86.28431105045972 chr4 191154276 778067671 4.0703649810062315 76.8066116646653 chr5 180915260 2011705790 11.119602569733477 259.8576730325882 chr6 171115067 790525087 4.619845001726236 57.18367382722757 chr7 159138663 2006986069 12.611555426980054 225.25035673259205 chr8 146364022 1812403583 12.382848996866183 206.24095165056156 chr9 141213431 893610130 6.3280817105845975 64.18308303367083 chr10 135534747 1333757564 9.840705749057841 94.12774969736665 chr11 135006516 1736379247 12.861447717086484 108.46845111894953 chr12 133851895 1495773311 11.174838510878011 100.4371120955879 chr13 115169878 206165163 1.7900962176933104 24.180770954593324 chr14 107349540 786162891 7.323393197586128 70.49497357341654 chr15 102531392 1999241626 19.498824574623935 174.48258584696615 chr16 90354753 2452467876 27.14265486398928 232.53088973090254 chr17 81195210 2372077880 29.21450514137472 206.90199163626806 chr18 78077248 200503382 2.5680129248407937 38.73505602672333 chr19 59128983 3417541905 57.79808364030208 298.63915461403724 chr20 63025520 1032827258 16.387445244402585 140.68218386397328 chr21 48129895 506861459 10.531114996199348 291.3903818781099 chr22 51304566 1129926748 22.023902278015566 178.3448185050461 chrMT 16571 63709 3.844608050208195 3.160315747717703 chrX 155270560 1453388421 9.360360528100111 92.63790882704814 chrY 59373566 33522910 0.5646100151707243 32.505631880803314