BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618645.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 = 43,856,208 number of mapped reads = 39,447,497 (89.95%) number of supplementary alignments = 234,023 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 21,098,979 number of mapped paired reads (second in pair) = 18,348,518 number of mapped paired reads (both in pair) = 36,185,496 number of mapped paired reads (singletons) = 3,262,001 number of mapped bases = 3,660,662,754 bp number of sequenced bases = 3,658,031,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,198,562 duplication rate = 19.54% >>>>>>> Insert size mean insert size = 176,524.5764 std insert size = 4,207,537.6727 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 52.4424 >>>>>>> ACTG content number of A's = 999,337,763 bp (27.32%) number of C's = 788,769,825 bp (21.56%) number of T's = 1,027,848,698 bp (28.1%) number of G's = 841,920,989 bp (23.02%) number of N's = 154,649 bp (0%) GC percentage = 44.58% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 49,900,306 number of insertions = 694,497 mapped reads with insertion percentage = 1.73% number of deletions = 1,884,090 mapped reads with deletion percentage = 4.65% homopolymer indels = 52.36% >>>>>>> Coverage mean coverageData = 1.1825X std coverageData = 5.2766X There is a 26.75% of reference with a coverageData >= 1X There is a 17.34% of reference with a coverageData >= 2X There is a 12.46% of reference with a coverageData >= 3X There is a 9.43% of reference with a coverageData >= 4X There is a 7.38% of reference with a coverageData >= 5X There is a 5.91% of reference with a coverageData >= 6X There is a 4.82% of reference with a coverageData >= 7X There is a 3.99% of reference with a coverageData >= 8X There is a 3.34% of reference with a coverageData >= 9X There is a 2.83% of reference with a coverageData >= 10X There is a 2.41% of reference with a coverageData >= 11X There is a 2.07% of reference with a coverageData >= 12X There is a 1.79% of reference with a coverageData >= 13X There is a 1.56% of reference with a coverageData >= 14X There is a 1.36% of reference with a coverageData >= 15X There is a 1.19% of reference with a coverageData >= 16X There is a 1.05% of reference with a coverageData >= 17X There is a 0.93% of reference with a coverageData >= 18X There is a 0.83% of reference with a coverageData >= 19X There is a 0.74% of reference with a coverageData >= 20X There is a 0.66% of reference with a coverageData >= 21X There is a 0.59% of reference with a coverageData >= 22X There is a 0.53% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.43% of reference with a coverageData >= 25X There is a 0.39% of reference with a coverageData >= 26X There is a 0.36% of reference with a coverageData >= 27X There is a 0.32% of reference with a coverageData >= 28X There is a 0.3% of reference with a coverageData >= 29X There is a 0.27% of reference with a coverageData >= 30X There is a 0.25% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.15% of reference with a coverageData >= 37X There is a 0.14% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.11% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.08% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.06% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 333385104 1.3375497427547032 6.654858080523069 chr2 243199373 318923748 1.3113674762640115 6.718084676863957 chr3 198022430 250421263 1.2646105948704902 4.527701635414713 chr4 191154276 199287522 1.0425480725317386 4.2742639876878625 chr5 180915260 219173169 1.211468667706638 4.578710736563028 chr6 171115067 210098378 1.2278192778897723 4.322829102328345 chr7 159138663 191767540 1.2050342536810177 4.6047908189502555 chr8 146364022 183760288 1.255501765317709 4.479904041834074 chr9 141213431 166767077 1.180957617268006 5.716011689400623 chr10 135534747 190038032 1.402135143986361 4.9537830658007325 chr11 135006516 190881867 1.413871512690543 5.578540788205347 chr12 133851895 170825345 1.2762265711665868 4.927884918562504 chr13 115169878 103745054 0.9008002422300039 3.724149773362745 chr14 107349540 117434229 1.0939425450728526 4.20305730695499 chr15 102531392 122990035 1.1995354066781811 4.902975178978143 chr16 90354753 130197696 1.4409612297872143 9.167780668726326 chr17 81195210 118640929 1.4611813800346105 5.232542675707724 chr18 78077248 97401113 1.2474967483485073 5.658877820140694 chr19 59128983 78829291 1.3331751537143806 6.437684685415571 chr20 63025520 104564221 1.6590774816296636 5.51573471150652 chr21 48129895 49207395 1.022387333277997 6.115879115747583 chr22 51304566 66165197 1.2896551351784167 5.3362281893036805 chrMT 16571 36235 2.1866513789149717 6.676498218797692 chrX 155270560 12655274 0.0815046587067117 2.0087874024158903 chrY 59373566 33466752 0.5636641733797831 4.338497955520673