BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975250.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 = 116,022,292 number of mapped reads = 115,473,156 (99.53%) number of supplementary alignments = 235,508 (0.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 57,725,168 number of mapped paired reads (second in pair) = 57,747,988 number of mapped paired reads (both in pair) = 115,207,452 number of mapped paired reads (singletons) = 265,704 number of mapped bases = 10,646,000,697 bp number of sequenced bases = 10,642,399,195 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,248,053 duplication rate = 49.68% >>>>>>> Insert size mean insert size = 58,677.3268 std insert size = 2,376,816.094 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 55.9365 >>>>>>> ACTG content number of A's = 2,855,245,259 bp (26.83%) number of C's = 2,304,529,788 bp (21.65%) number of T's = 2,995,440,056 bp (28.15%) number of G's = 2,486,873,677 bp (23.37%) number of N's = 310,415 bp (0%) GC percentage = 45.02% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 62,675,177 number of insertions = 1,182,918 mapped reads with insertion percentage = 1.01% number of deletions = 2,437,326 mapped reads with deletion percentage = 2.08% homopolymer indels = 45.28% >>>>>>> Coverage mean coverageData = 3.439X std coverageData = 45.5712X There is a 21.53% of reference with a coverageData >= 1X There is a 12.2% of reference with a coverageData >= 2X There is a 7.31% of reference with a coverageData >= 3X There is a 5.31% of reference with a coverageData >= 4X There is a 4.04% of reference with a coverageData >= 5X There is a 3.41% of reference with a coverageData >= 6X There is a 2.97% of reference with a coverageData >= 7X There is a 2.7% of reference with a coverageData >= 8X There is a 2.5% of reference with a coverageData >= 9X There is a 2.36% of reference with a coverageData >= 10X There is a 2.24% of reference with a coverageData >= 11X There is a 2.15% of reference with a coverageData >= 12X There is a 2.08% of reference with a coverageData >= 13X There is a 2.01% of reference with a coverageData >= 14X There is a 1.96% of reference with a coverageData >= 15X There is a 1.9% of reference with a coverageData >= 16X There is a 1.86% of reference with a coverageData >= 17X There is a 1.81% of reference with a coverageData >= 18X There is a 1.77% of reference with a coverageData >= 19X There is a 1.74% of reference with a coverageData >= 20X There is a 1.7% of reference with a coverageData >= 21X There is a 1.67% of reference with a coverageData >= 22X There is a 1.64% of reference with a coverageData >= 23X There is a 1.61% of reference with a coverageData >= 24X There is a 1.58% of reference with a coverageData >= 25X There is a 1.55% of reference with a coverageData >= 26X There is a 1.53% of reference with a coverageData >= 27X There is a 1.5% of reference with a coverageData >= 28X There is a 1.48% of reference with a coverageData >= 29X There is a 1.46% of reference with a coverageData >= 30X There is a 1.44% of reference with a coverageData >= 31X There is a 1.41% of reference with a coverageData >= 32X There is a 1.39% of reference with a coverageData >= 33X There is a 1.37% of reference with a coverageData >= 34X There is a 1.36% of reference with a coverageData >= 35X There is a 1.34% of reference with a coverageData >= 36X There is a 1.32% of reference with a coverageData >= 37X There is a 1.3% of reference with a coverageData >= 38X There is a 1.29% of reference with a coverageData >= 39X There is a 1.27% of reference with a coverageData >= 40X There is a 1.25% of reference with a coverageData >= 41X There is a 1.24% of reference with a coverageData >= 42X There is a 1.22% of reference with a coverageData >= 43X There is a 1.21% of reference with a coverageData >= 44X There is a 1.19% of reference with a coverageData >= 45X There is a 1.18% of reference with a coverageData >= 46X There is a 1.17% of reference with a coverageData >= 47X There is a 1.15% of reference with a coverageData >= 48X There is a 1.14% of reference with a coverageData >= 49X There is a 1.13% of reference with a coverageData >= 50X There is a 1.12% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1181764669 4.741270710816003 54.01332014588564 chr2 243199373 801244519 3.2945994437247172 40.779269386046565 chr3 198022430 665483009 3.360644594655262 41.79641443425395 chr4 191154276 480404325 2.5131759281178727 60.5361311040118 chr5 180915260 497991470 2.752622802520915 36.54544824841982 chr6 171115067 926712998 5.415729977769871 66.8070056835854 chr7 159138663 516961502 3.248497205232898 43.6560954122424 chr8 146364022 354090855 2.4192479146275443 32.01094868449951 chr9 141213431 393983097 2.7899831780165445 34.88007423572718 chr10 135534747 443484629 3.2721102065435663 41.919151078647666 chr11 135006516 623918543 4.621395777667502 52.48735860660166 chr12 133851895 531826572 3.9732464900851796 42.91431493243777 chr13 115169878 272709355 2.3678878517176165 37.46127265536755 chr14 107349540 342123662 3.1870063160028446 40.35726367928913 chr15 102531392 293763511 2.865107995412761 34.77650458819607 chr16 90354753 356935126 3.9503746526759915 46.7402701711721 chr17 81195210 462090912 5.691110497774438 57.545732419640615 chr18 78077248 230821175 2.9563180172538868 42.349822367908324 chr19 59128983 360070828 6.089582633274785 59.276033946376785 chr20 63025520 245650735 3.8976391626756905 49.201086627165125 chr21 48129895 93882998 1.9506171372283276 30.957881751772206 chr22 51304566 128240008 2.4995827466896414 31.892671536217275 chrMT 16571 214946 12.971214772795848 23.69793251687648 chrX 155270560 428424185 2.759210664275314 38.74182491754562 chrY 59373566 13207068 0.22244020175577797 5.380070311429702