BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618602.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 58,190,958 number of mapped reads = 53,093,407 (91.24%) number of supplementary alignments = 141,643 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 27,161,128 number of mapped paired reads (second in pair) = 25,932,279 number of mapped paired reads (both in pair) = 51,209,814 number of mapped paired reads (singletons) = 1,883,593 number of mapped bases = 5,011,605,053 bp number of sequenced bases = 5,008,518,083 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,383,334 duplication rate = 38.19% >>>>>>> Insert size mean insert size = 71,551.8917 std insert size = 2,701,591.6443 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7839 >>>>>>> ACTG content number of A's = 1,309,473,598 bp (26.14%) number of C's = 1,155,093,980 bp (23.06%) number of T's = 1,324,222,019 bp (26.44%) number of G's = 1,219,549,440 bp (24.35%) number of N's = 179,046 bp (0%) GC percentage = 47.41% >>>>>>> Mismatches and indels general error rate = 0.0128 number of mismatches = 62,599,362 number of insertions = 875,470 mapped reads with insertion percentage = 1.62% number of deletions = 2,226,932 mapped reads with deletion percentage = 4.1% homopolymer indels = 52.62% >>>>>>> Coverage mean coverageData = 1.6189X std coverageData = 8.0351X There is a 21.12% of reference with a coverageData >= 1X There is a 15.49% of reference with a coverageData >= 2X There is a 12.31% of reference with a coverageData >= 3X There is a 10.27% of reference with a coverageData >= 4X There is a 8.72% of reference with a coverageData >= 5X There is a 7.56% of reference with a coverageData >= 6X There is a 6.61% of reference with a coverageData >= 7X There is a 5.85% of reference with a coverageData >= 8X There is a 5.2% of reference with a coverageData >= 9X There is a 4.66% of reference with a coverageData >= 10X There is a 4.19% of reference with a coverageData >= 11X There is a 3.79% of reference with a coverageData >= 12X There is a 3.44% of reference with a coverageData >= 13X There is a 3.14% of reference with a coverageData >= 14X There is a 2.87% of reference with a coverageData >= 15X There is a 2.63% of reference with a coverageData >= 16X There is a 2.42% of reference with a coverageData >= 17X There is a 2.23% of reference with a coverageData >= 18X There is a 2.06% of reference with a coverageData >= 19X There is a 1.91% of reference with a coverageData >= 20X There is a 1.77% of reference with a coverageData >= 21X There is a 1.65% of reference with a coverageData >= 22X There is a 1.54% of reference with a coverageData >= 23X There is a 1.43% of reference with a coverageData >= 24X There is a 1.34% of reference with a coverageData >= 25X There is a 1.25% of reference with a coverageData >= 26X There is a 1.17% of reference with a coverageData >= 27X There is a 1.1% of reference with a coverageData >= 28X There is a 1.04% of reference with a coverageData >= 29X There is a 0.97% of reference with a coverageData >= 30X There is a 0.92% of reference with a coverageData >= 31X There is a 0.87% of reference with a coverageData >= 32X There is a 0.82% of reference with a coverageData >= 33X There is a 0.77% of reference with a coverageData >= 34X There is a 0.73% of reference with a coverageData >= 35X There is a 0.69% of reference with a coverageData >= 36X There is a 0.65% of reference with a coverageData >= 37X There is a 0.62% of reference with a coverageData >= 38X There is a 0.59% of reference with a coverageData >= 39X There is a 0.56% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.51% of reference with a coverageData >= 42X There is a 0.48% of reference with a coverageData >= 43X There is a 0.46% of reference with a coverageData >= 44X There is a 0.44% of reference with a coverageData >= 45X There is a 0.42% of reference with a coverageData >= 46X There is a 0.4% of reference with a coverageData >= 47X There is a 0.38% of reference with a coverageData >= 48X There is a 0.36% of reference with a coverageData >= 49X There is a 0.35% of reference with a coverageData >= 50X There is a 0.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 464889357 1.8651482396908452 8.508303638485646 chr2 243199373 403352720 1.658526973258274 8.95535248841538 chr3 198022430 307018812 1.550424424142255 6.596481348239777 chr4 191154276 214939672 1.1244303632527686 7.399765681396295 chr5 180915260 264556420 1.4623223049288379 6.205688422672128 chr6 171115067 256230557 1.4974166886192435 6.274043855176473 chr7 159138663 239421979 1.5044865558534948 6.710509679533322 chr8 146364022 238702711 1.6308837905533915 10.51546654385958 chr9 141213431 221073092 1.5655245427752549 7.704153160268779 chr10 135534747 256101479 1.8895632645405682 7.90320061654955 chr11 135006516 268775102 1.9908305907249693 8.214068792812464 chr12 133851895 218988742 1.6360526087434175 7.0469477156740155 chr13 115169878 118929182 1.0326413821502876 5.070628484889773 chr14 107349540 153776102 1.43248030685553 6.556526046698245 chr15 102531392 164889083 1.6081814533445522 7.05444334707678 chr16 90354753 197461860 2.1854064500624557 15.851356013401444 chr17 81195210 191272907 2.355716636486315 8.813117147966285 chr18 78077248 118868633 1.522449062241538 7.011483493797593 chr19 59128983 141841764 2.398853435378721 9.60538364954121 chr20 63025520 158242706 2.5107719222308678 9.137393556469023 chr21 48129895 66151159 1.3744297385232194 11.044446724542722 chr22 51304566 109595975 2.1361836488393644 8.959143268707537 chrMT 16571 51253 3.09293343793374 18.411075981818858 chrX 155270560 229137136 1.475728148336684 5.998067353863507 chrY 59373566 7336650 0.12356761593197889 4.6756592861157245