BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617507.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 = 423,767,428 number of mapped reads = 416,354,942 (98.25%) number of supplementary alignments = 1,846,413 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 208,241,872 number of mapped paired reads (second in pair) = 208,113,070 number of mapped paired reads (both in pair) = 414,857,932 number of mapped paired reads (singletons) = 1,497,010 number of mapped bases = 40,890,919,965 bp number of sequenced bases = 40,866,472,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 185,332,729 duplication rate = 19.75% >>>>>>> Insert size mean insert size = 23,080.7293 std insert size = 1,366,950.6952 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.9306 >>>>>>> ACTG content number of A's = 12,096,360,989 bp (29.6%) number of C's = 8,235,869,723 bp (20.15%) number of T's = 12,116,716,277 bp (29.65%) number of G's = 8,413,486,136 bp (20.59%) number of N's = 4,039,529 bp (0.01%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 406,559,275 number of insertions = 6,079,053 mapped reads with insertion percentage = 1.43% number of deletions = 14,297,135 mapped reads with deletion percentage = 3.36% homopolymer indels = 47.68% >>>>>>> Coverage mean coverageData = 13.209X std coverageData = 138.4813X There is a 75.54% of reference with a coverageData >= 1X There is a 68.54% of reference with a coverageData >= 2X There is a 62.79% of reference with a coverageData >= 3X There is a 57.88% of reference with a coverageData >= 4X There is a 53.55% of reference with a coverageData >= 5X There is a 49.69% of reference with a coverageData >= 6X There is a 46.2% of reference with a coverageData >= 7X There is a 43.04% of reference with a coverageData >= 8X There is a 40.16% of reference with a coverageData >= 9X There is a 37.53% of reference with a coverageData >= 10X There is a 35.11% of reference with a coverageData >= 11X There is a 32.9% of reference with a coverageData >= 12X There is a 30.85% of reference with a coverageData >= 13X There is a 28.97% of reference with a coverageData >= 14X There is a 27.22% of reference with a coverageData >= 15X There is a 25.61% of reference with a coverageData >= 16X There is a 24.11% of reference with a coverageData >= 17X There is a 22.72% of reference with a coverageData >= 18X There is a 21.43% of reference with a coverageData >= 19X There is a 20.23% of reference with a coverageData >= 20X There is a 19.11% of reference with a coverageData >= 21X There is a 18.07% of reference with a coverageData >= 22X There is a 17.09% of reference with a coverageData >= 23X There is a 16.18% of reference with a coverageData >= 24X There is a 15.33% of reference with a coverageData >= 25X There is a 14.53% of reference with a coverageData >= 26X There is a 13.78% of reference with a coverageData >= 27X There is a 13.08% of reference with a coverageData >= 28X There is a 12.42% of reference with a coverageData >= 29X There is a 11.8% of reference with a coverageData >= 30X There is a 11.22% of reference with a coverageData >= 31X There is a 10.68% of reference with a coverageData >= 32X There is a 10.16% of reference with a coverageData >= 33X There is a 9.68% of reference with a coverageData >= 34X There is a 9.22% of reference with a coverageData >= 35X There is a 8.79% of reference with a coverageData >= 36X There is a 8.39% of reference with a coverageData >= 37X There is a 8% of reference with a coverageData >= 38X There is a 7.64% of reference with a coverageData >= 39X There is a 7.3% of reference with a coverageData >= 40X There is a 6.97% of reference with a coverageData >= 41X There is a 6.67% of reference with a coverageData >= 42X There is a 6.38% of reference with a coverageData >= 43X There is a 6.1% of reference with a coverageData >= 44X There is a 5.84% of reference with a coverageData >= 45X There is a 5.59% of reference with a coverageData >= 46X There is a 5.36% of reference with a coverageData >= 47X There is a 5.14% of reference with a coverageData >= 48X There is a 4.92% of reference with a coverageData >= 49X There is a 4.72% of reference with a coverageData >= 50X There is a 4.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2625554535 10.533793354119668 133.93755579535792 chr2 243199373 4233302781 17.406717495936967 163.09628663805657 chr3 198022430 3380290882 17.070242406377904 26.529953235566623 chr4 191154276 2123243446 11.107486007794039 86.44493569803574 chr5 180915260 2622245562 14.494330450620915 24.919190928711256 chr6 171115067 1929541935 11.276283081489254 75.28496165645191 chr7 159138663 3160862884 19.862318963933987 187.72880736319274 chr8 146364022 1817365340 12.416749110652344 52.6773794261533 chr9 141213431 1699109555 12.032209280433106 269.0195256315094 chr10 135534747 1732540924 12.783001867410428 264.1413207512087 chr11 135006516 2306446669 17.08396555466997 183.73771521094739 chr12 133851895 1783782502 13.326539022850591 23.43389376243895 chr13 115169878 1740968957 15.1165303570088 25.134807118251945 chr14 107349540 1187056733 11.057865110553804 27.856940101549704 chr15 102531392 918793139 8.961091048095787 16.269011355798746 chr16 90354753 1097629869 12.148003647356548 207.24899913381472 chr17 81195210 1133860561 13.964623787536235 197.3659963980863 chr18 78077248 738564878 9.459412273342421 246.99791644698098 chr19 59128983 480516165 8.12657584521621 81.89706825108271 chr20 63025520 1194606410 18.954328500581987 34.827529487991264 chr21 48129895 589001349 12.237744316707943 51.153236011100134 chr22 51304566 298966218 5.827282858215778 14.093302264407306 chrMT 16571 28223714 1703.1992034276748 1238.2550883293911 chrX 155270560 1926704514 12.408691731388101 56.85269071358207 chrY 59373566 141740443 2.3872651172745796 194.3247361559827