BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617487.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,569,275 (95.53%) number of supplementary alignments = 137,514 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,427,302 number of mapped paired reads (second in pair) = 15,141,973 number of mapped paired reads (both in pair) = 30,033,288 number of mapped paired reads (singletons) = 535,987 number of mapped bases = 2,985,952,162 bp number of sequenced bases = 2,984,174,285 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,307,837 duplication rate = 9.97% >>>>>>> Insert size mean insert size = 29,068.2067 std insert size = 1,562,899.2539 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 52.7969 >>>>>>> ACTG content number of A's = 879,780,462 bp (29.48%) number of C's = 603,548,068 bp (20.22%) number of T's = 879,362,833 bp (29.47%) number of G's = 618,604,027 bp (20.73%) number of N's = 2,878,895 bp (0.1%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 36,092,553 number of insertions = 443,983 mapped reads with insertion percentage = 1.42% number of deletions = 1,041,549 mapped reads with deletion percentage = 3.34% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.9646X std coverageData = 9.7626X There is a 38.33% of reference with a coverageData >= 1X There is a 20.71% of reference with a coverageData >= 2X There is a 11.71% of reference with a coverageData >= 3X There is a 6.97% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 2.76% of reference with a coverageData >= 6X There is a 1.83% of reference with a coverageData >= 7X There is a 1.25% of reference with a coverageData >= 8X There is a 0.88% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192390193 0.7718744780980906 9.375283942067972 chr2 243199373 308529640 1.2686284351563686 11.460900587253146 chr3 198022430 246323958 1.2439194792226316 2.2348549781528706 chr4 191154276 154202854 0.8066931968605295 6.182798030542611 chr5 180915260 191473088 1.05835786323387 2.092013458418795 chr6 171115067 140625524 0.8218184784394235 5.418540403204018 chr7 159138663 230388891 1.4477241837830446 13.290336871306787 chr8 146364022 132597503 0.9059432857071938 3.898294480546926 chr9 141213431 124165686 0.8792767452835276 18.716851379980643 chr10 135534747 126393389 0.9325533990187771 18.80069024697674 chr11 135006516 168157587 1.2455516369298798 12.66282106953113 chr12 133851895 130549929 0.975331197216147 1.968401961841986 chr13 115169878 126654385 1.099717974868394 2.1217042394630297 chr14 107349540 86986226 0.8103083254944549 2.2133182162496707 chr15 102531392 67380410 0.657168586963103 1.4471269493288665 chr16 90354753 80332297 0.8890766045257188 14.847322407693367 chr17 81195210 83400710 1.0271629323946572 13.718254628908609 chr18 78077248 53511180 0.6853620148087187 16.996051812989624 chr19 59128983 35581032 0.6017528155354879 5.918475091667992 chr20 63025520 88315215 1.4012611875316539 2.8069644453496636 chr21 48129895 42857321 0.8904511634608802 3.823907212391299 chr22 51304566 22355492 0.4357407876718029 1.258618584836644 chrMT 16571 2096898 126.54022086778106 96.21155968423204 chrX 155270560 140345038 0.9038741020834857 4.192117423456138 chrY 59373566 10337716 0.17411310615906075 13.915314041922015