BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975327.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 = 4,037,040 number of mapped reads = 3,966,416 (98.25%) number of supplementary alignments = 20,634 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,981,869 number of mapped paired reads (second in pair) = 1,984,547 number of mapped paired reads (both in pair) = 3,944,046 number of mapped paired reads (singletons) = 22,370 number of mapped bases = 362,215,030 bp number of sequenced bases = 361,999,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 355,722 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 44,884.3318 std insert size = 1,970,946.83 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 52.3586 >>>>>>> ACTG content number of A's = 105,658,439 bp (29.19%) number of C's = 70,273,360 bp (19.41%) number of T's = 107,776,351 bp (29.77%) number of G's = 78,283,977 bp (21.63%) number of N's = 7,022 bp (0%) GC percentage = 41.04% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 3,155,847 number of insertions = 67,621 mapped reads with insertion percentage = 1.66% number of deletions = 117,467 mapped reads with deletion percentage = 2.9% homopolymer indels = 44.72% >>>>>>> Coverage mean coverageData = 0.117X std coverageData = 2.6497X There is a 7.61% of reference with a coverageData >= 1X There is a 2.24% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 26858928 0.10775872048880472 2.106110180446919 chr2 243199373 31827015 0.13086799775589883 1.8988457444032856 chr3 198022430 23651337 0.11943766673300596 0.726827638469337 chr4 191154276 25435837 0.13306444162410472 2.496792768475928 chr5 180915260 21707776 0.11998863998537215 0.4639223000161578 chr6 171115067 20085441 0.11737973372035088 1.4785123321638383 chr7 159138663 19018755 0.11951058681446884 2.4699119804045084 chr8 146364022 17634220 0.1204819310035085 0.6798039519419149 chr9 141213431 14451684 0.10233930227217551 2.126338701839826 chr10 135534747 24654116 0.18190254931453112 9.885917609999806 chr11 135006516 17112259 0.1267513562086144 1.8894560691817035 chr12 133851895 15277823 0.1141397587236251 0.4487982285843181 chr13 115169878 10293105 0.08937323872132608 0.38281172386604906 chr14 107349540 9987293 0.09303526591730156 0.5012344675444793 chr15 102531392 9242320 0.09014136860640691 0.3894459471924548 chr16 90354753 13741698 0.15208605572747236 3.527194686718845 chr17 81195210 7732342 0.09523150442002674 1.4797330523364673 chr18 78077248 9950392 0.12744291397155802 2.658762837670207 chr19 59128983 4348422 0.07354129530690558 1.2116786485361222 chr20 63025520 7048000 0.11182771677250739 0.7235955477045976 chr21 48129895 4490983 0.0933096363497157 1.036089077870167 chr22 51304566 3027332 0.05900706771401204 0.32082520444664653 chrMT 16571 60862 3.672801882807314 2.8640192440934347 chrX 155270560 22740391 0.14645655300013086 0.9778458827743113 chrY 59373566 1836699 0.030934625014775095 2.4951052469720456