BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975258.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 70,102,960 number of mapped reads = 70,022,072 (99.88%) number of supplementary alignments = 154,094 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 35,011,442 number of mapped paired reads (second in pair) = 35,010,630 number of mapped paired reads (both in pair) = 69,995,000 number of mapped paired reads (singletons) = 27,072 number of mapped bases = 6,855,960,513 bp number of sequenced bases = 6,855,207,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,028,964 duplication rate = 42.2% >>>>>>> Insert size mean insert size = 79,592.9614 std insert size = 2,786,696.6608 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 56.2443 >>>>>>> ACTG content number of A's = 1,773,263,849 bp (25.87%) number of C's = 1,660,732,914 bp (24.23%) number of T's = 1,770,481,420 bp (25.83%) number of G's = 1,650,604,207 bp (24.08%) number of N's = 125,373 bp (0%) GC percentage = 48.3% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 19,248,097 number of insertions = 570,484 mapped reads with insertion percentage = 0.81% number of deletions = 344,835 mapped reads with deletion percentage = 0.48% homopolymer indels = 32.04% >>>>>>> Coverage mean coverageData = 2.2147X std coverageData = 17.7927X There is a 12.71% of reference with a coverageData >= 1X There is a 6.56% of reference with a coverageData >= 2X There is a 4.56% of reference with a coverageData >= 3X There is a 3.93% of reference with a coverageData >= 4X There is a 3.56% of reference with a coverageData >= 5X There is a 3.35% of reference with a coverageData >= 6X There is a 3.18% of reference with a coverageData >= 7X There is a 3.05% of reference with a coverageData >= 8X There is a 2.95% of reference with a coverageData >= 9X There is a 2.85% of reference with a coverageData >= 10X There is a 2.77% of reference with a coverageData >= 11X There is a 2.69% of reference with a coverageData >= 12X There is a 2.62% of reference with a coverageData >= 13X There is a 2.55% of reference with a coverageData >= 14X There is a 2.49% of reference with a coverageData >= 15X There is a 2.43% of reference with a coverageData >= 16X There is a 2.38% of reference with a coverageData >= 17X There is a 2.33% of reference with a coverageData >= 18X There is a 2.28% of reference with a coverageData >= 19X There is a 2.23% of reference with a coverageData >= 20X There is a 2.19% of reference with a coverageData >= 21X There is a 2.14% of reference with a coverageData >= 22X There is a 2.1% of reference with a coverageData >= 23X There is a 2.06% of reference with a coverageData >= 24X There is a 2.02% of reference with a coverageData >= 25X There is a 1.99% of reference with a coverageData >= 26X There is a 1.95% of reference with a coverageData >= 27X There is a 1.92% of reference with a coverageData >= 28X There is a 1.88% of reference with a coverageData >= 29X There is a 1.85% of reference with a coverageData >= 30X There is a 1.82% of reference with a coverageData >= 31X There is a 1.79% of reference with a coverageData >= 32X There is a 1.76% of reference with a coverageData >= 33X There is a 1.73% of reference with a coverageData >= 34X There is a 1.7% of reference with a coverageData >= 35X There is a 1.67% of reference with a coverageData >= 36X There is a 1.65% of reference with a coverageData >= 37X There is a 1.62% of reference with a coverageData >= 38X There is a 1.59% of reference with a coverageData >= 39X There is a 1.57% of reference with a coverageData >= 40X There is a 1.54% of reference with a coverageData >= 41X There is a 1.52% of reference with a coverageData >= 42X There is a 1.49% of reference with a coverageData >= 43X There is a 1.47% of reference with a coverageData >= 44X There is a 1.45% of reference with a coverageData >= 45X There is a 1.42% of reference with a coverageData >= 46X There is a 1.4% of reference with a coverageData >= 47X There is a 1.38% of reference with a coverageData >= 48X There is a 1.36% of reference with a coverageData >= 49X There is a 1.34% of reference with a coverageData >= 50X There is a 1.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 686528948 2.754372066338804 20.26406365988763 chr2 243199373 525353355 2.1601756144330193 17.369852973932296 chr3 198022430 422824910 2.13523745769608 17.213302463676904 chr4 191154276 299982315 1.56932045297276 15.077460063318565 chr5 180915260 333291801 1.8422536661639266 16.099472037457957 chr6 171115067 385571021 2.2532850423978155 18.74225577125531 chr7 159138663 332033667 2.086442481925338 17.58044140046814 chr8 146364022 241877196 1.652572761357979 14.696178770943385 chr9 141213431 270615643 1.916359096182572 16.166118893170776 chr10 135534747 277722391 2.0490862833867984 16.8871974713214 chr11 135006516 409031921 3.0297198470035327 21.65764423575035 chr12 133851895 368248735 2.7511656446851203 19.815244808145653 chr13 115169878 138489704 1.2024819892576426 12.811015503802313 chr14 107349540 221161087 2.0601959449476914 17.185339701379338 chr15 102531392 231658224 2.2593882661809563 17.46295228386909 chr16 90354753 248792228 2.7535045998078265 19.120224015382846 chr17 81195210 353893872 4.358556028120378 24.60270198670303 chr18 78077248 111557703 1.428811924826039 13.82269944911927 chr19 59128983 346989589 5.868350365505187 27.605534359864148 chr20 63025520 161884549 2.5685555470228567 18.87711622145002 chr21 48129895 72041016 1.4968039302807539 15.79898370902846 chr22 51304566 126635841 2.4683152177917265 17.279444208029304 chrMT 16571 472820 28.532979301188824 61.791257185085996 chrX 155270560 288102332 1.8554858821917046 17.387115018122863 chrY 59373566 1199645 0.02020503535192749 0.7413440824920744