BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618663.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 = 23,960,773 number of mapped reads = 22,626,768 (94.43%) number of supplementary alignments = 68,914 (0.29%) number of secondary alignments = 0 number of mapped bases = 2,210,136,229 bp number of sequenced bases = 2,208,589,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,426,767 duplication rate = 17.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.8566 >>>>>>> ACTG content number of A's = 601,154,384 bp (27.22%) number of C's = 488,918,261 bp (22.14%) number of T's = 611,942,921 bp (27.71%) number of G's = 484,573,035 bp (21.94%) number of N's = 22,000,826 bp (1%) GC percentage = 44.08% >>>>>>> Mismatches and indels general error rate = 0.0197 number of mismatches = 42,835,754 number of insertions = 412,923 mapped reads with insertion percentage = 1.79% number of deletions = 1,099,338 mapped reads with deletion percentage = 4.74% homopolymer indels = 52.84% >>>>>>> Coverage mean coverageData = 0.7139X std coverageData = 3.2257X There is a 20.58% of reference with a coverageData >= 1X There is a 12.27% of reference with a coverageData >= 2X There is a 8.19% of reference with a coverageData >= 3X There is a 5.82% of reference with a coverageData >= 4X There is a 4.32% of reference with a coverageData >= 5X There is a 3.3% of reference with a coverageData >= 6X There is a 2.59% of reference with a coverageData >= 7X There is a 2.07% of reference with a coverageData >= 8X There is a 1.68% of reference with a coverageData >= 9X There is a 1.38% of reference with a coverageData >= 10X There is a 1.14% of reference with a coverageData >= 11X There is a 0.96% of reference with a coverageData >= 12X There is a 0.81% of reference with a coverageData >= 13X There is a 0.69% of reference with a coverageData >= 14X There is a 0.59% of reference with a coverageData >= 15X There is a 0.51% of reference with a coverageData >= 16X There is a 0.44% of reference with a coverageData >= 17X There is a 0.38% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.3% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.16% of reference with a coverageData >= 25X There is a 0.14% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.08% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.06% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% 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 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 207287335 0.8316422008031827 3.383524680469807 chr2 243199373 192762542 0.7926111799638562 4.511567975745042 chr3 198022430 147809125 0.7464261750550177 2.440503701186902 chr4 191154276 114522344 0.5991095067106947 2.5161454173933717 chr5 180915260 132369596 0.7316662839828989 2.4157494776927693 chr6 171115067 123025155 0.718961557020575 2.4796231846856958 chr7 159138663 114851932 0.7217097959406634 2.4814263838676585 chr8 146364022 112306379 0.7673086422836891 2.49499680180726 chr9 141213431 98422062 0.6969738027256062 2.6888368991833227 chr10 135534747 115909664 0.8552025703047205 2.7525757912919366 chr11 135006516 116761366 0.8648572636301495 2.992425589853112 chr12 133851895 101238970 0.7563506665333353 2.6281136506059872 chr13 115169878 61964543 0.5380273390582214 2.048573117919927 chr14 107349540 69241120 0.6450062105529283 2.363219852042108 chr15 102531392 74187447 0.7235583712742337 2.5172311381128307 chr16 90354753 80112264 0.8866413922906745 8.984847551460367 chr17 81195210 75054143 0.9243666344357013 3.1066627479082456 chr18 78077248 58476074 0.7489515255455725 2.919591804158277 chr19 59128983 50798122 0.8591069797361474 3.3074595087673866 chr20 63025520 66001352 1.0472163022217031 3.259444662250175 chr21 48129895 30233172 0.628157863215783 4.072351219514479 chr22 51304566 40261195 0.7847487687548121 3.0096429349095213 chrMT 16571 6588 0.397562005913946 1.1870812690628805 chrX 155270560 5985100 0.038546264018111356 0.7050032009395482 chrY 59373566 20548639 0.3460906996894881 3.161326755427758