BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617377.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 = 30,478,284 (95.24%) number of supplementary alignments = 67,099 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,300,521 number of mapped paired reads (second in pair) = 15,177,763 number of mapped paired reads (both in pair) = 30,045,148 number of mapped paired reads (singletons) = 433,136 number of mapped bases = 2,995,430,600 bp number of sequenced bases = 2,994,548,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,578,545 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 54,303.4967 std insert size = 2,218,935.3454 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 53.5005 >>>>>>> ACTG content number of A's = 906,401,540 bp (30.27%) number of C's = 594,366,732 bp (19.85%) number of T's = 894,663,979 bp (29.88%) number of G's = 597,624,509 bp (19.96%) number of N's = 1,491,265 bp (0.05%) GC percentage = 39.81% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 30,998,173 number of insertions = 300,461 mapped reads with insertion percentage = 0.96% number of deletions = 365,056 mapped reads with deletion percentage = 1.16% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.9676X std coverageData = 9.8549X There is a 53.45% of reference with a coverageData >= 1X There is a 24.27% of reference with a coverageData >= 2X There is a 9.37% of reference with a coverageData >= 3X There is a 3.3% of reference with a coverageData >= 4X There is a 1.13% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 194607934 0.7807721129007739 19.94311494043603 chr2 243199373 295456655 1.2148742464068771 8.898925822998772 chr3 198022430 238431472 1.2040629538785077 1.4676964610390681 chr4 191154276 164019211 0.8580462568360229 9.523167665376969 chr5 180915260 188188568 1.0402028441381894 1.4704532064316589 chr6 171115067 140387859 0.8204295592509104 3.7563771251815705 chr7 159138663 243542121 1.530376819868092 10.991933802079812 chr8 146364022 126265283 0.8626797847902813 7.770040832970487 chr9 141213431 126201317 0.8936920242381194 15.057095065207426 chr10 135534747 126065192 0.9301319018952388 20.281547389190834 chr11 135006516 160972576 1.1923319019653837 5.56330493377675 chr12 133851895 132160208 0.9873615013070977 1.3477838488974947 chr13 115169878 130449455 1.1326699069699457 1.2997809768113924 chr14 107349540 86629439 0.8069847248530362 1.3903074955105994 chr15 102531392 67210979 0.6555161076911937 0.9785071762274582 chr16 90354753 75307547 0.8334652522374778 7.9701874493404485 chr17 81195210 93083460 1.1464156567856651 7.16671022072492 chr18 78077248 54244605 0.6947555964062668 15.481375647855762 chr19 59128983 55561552 0.9396669650144329 9.431062119624597 chr20 63025520 85720397 1.3600902777160744 2.4676852778983944 chr21 48129895 47449023 0.9858534492959106 3.2639710953759002 chr22 51304566 26683612 0.5201020899387395 0.9273570012191034 chrMT 16571 2034403 122.76887333293102 18.81607614308745 chrX 155270560 124507035 0.801871488065735 3.0023761670981006 chrY 59373566 10250697 0.1726474876041638 8.482256115567415