BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975313.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 = 77,739,668 number of mapped reads = 77,576,453 (99.79%) number of supplementary alignments = 129,989 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 38,809,468 number of mapped paired reads (second in pair) = 38,766,985 number of mapped paired reads (both in pair) = 77,494,964 number of mapped paired reads (singletons) = 81,489 number of mapped bases = 7,184,720,088 bp number of sequenced bases = 7,182,330,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,181,884 duplication rate = 44.95% >>>>>>> Insert size mean insert size = 85,902.3948 std insert size = 2,891,427.9697 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 56.0273 >>>>>>> ACTG content number of A's = 1,871,409,116 bp (26.06%) number of C's = 1,612,116,360 bp (22.45%) number of T's = 1,964,025,721 bp (27.35%) number of G's = 1,734,460,978 bp (24.15%) number of N's = 318,435 bp (0%) GC percentage = 46.59% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 44,215,796 number of insertions = 687,857 mapped reads with insertion percentage = 0.88% number of deletions = 1,670,364 mapped reads with deletion percentage = 2.12% homopolymer indels = 47.19% >>>>>>> Coverage mean coverageData = 2.3209X std coverageData = 26.5766X There is a 17.02% of reference with a coverageData >= 1X There is a 8.72% of reference with a coverageData >= 2X There is a 5.12% of reference with a coverageData >= 3X There is a 3.82% of reference with a coverageData >= 4X There is a 3.06% of reference with a coverageData >= 5X There is a 2.68% of reference with a coverageData >= 6X There is a 2.43% of reference with a coverageData >= 7X There is a 2.26% of reference with a coverageData >= 8X There is a 2.14% of reference with a coverageData >= 9X There is a 2.04% of reference with a coverageData >= 10X There is a 1.96% of reference with a coverageData >= 11X There is a 1.89% of reference with a coverageData >= 12X There is a 1.83% of reference with a coverageData >= 13X There is a 1.77% of reference with a coverageData >= 14X There is a 1.72% of reference with a coverageData >= 15X There is a 1.68% of reference with a coverageData >= 16X There is a 1.64% of reference with a coverageData >= 17X There is a 1.6% of reference with a coverageData >= 18X There is a 1.56% of reference with a coverageData >= 19X There is a 1.53% of reference with a coverageData >= 20X There is a 1.5% of reference with a coverageData >= 21X There is a 1.46% of reference with a coverageData >= 22X There is a 1.44% of reference with a coverageData >= 23X There is a 1.41% of reference with a coverageData >= 24X There is a 1.38% of reference with a coverageData >= 25X There is a 1.36% of reference with a coverageData >= 26X There is a 1.33% of reference with a coverageData >= 27X There is a 1.31% of reference with a coverageData >= 28X There is a 1.29% of reference with a coverageData >= 29X There is a 1.26% of reference with a coverageData >= 30X There is a 1.24% of reference with a coverageData >= 31X There is a 1.22% of reference with a coverageData >= 32X There is a 1.2% of reference with a coverageData >= 33X There is a 1.18% of reference with a coverageData >= 34X There is a 1.17% of reference with a coverageData >= 35X There is a 1.15% of reference with a coverageData >= 36X There is a 1.13% of reference with a coverageData >= 37X There is a 1.12% of reference with a coverageData >= 38X There is a 1.1% of reference with a coverageData >= 39X There is a 1.08% of reference with a coverageData >= 40X There is a 1.07% of reference with a coverageData >= 41X There is a 1.05% of reference with a coverageData >= 42X There is a 1.04% of reference with a coverageData >= 43X There is a 1.03% of reference with a coverageData >= 44X There is a 1.01% of reference with a coverageData >= 45X There is a 1% of reference with a coverageData >= 46X There is a 0.99% of reference with a coverageData >= 47X There is a 0.97% of reference with a coverageData >= 48X There is a 0.96% of reference with a coverageData >= 49X There is a 0.95% of reference with a coverageData >= 50X There is a 0.94% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 790044855 3.1696805882782533 32.9427265154906 chr2 243199373 527110408 2.167400357565889 23.734459681060905 chr3 198022430 484986053 2.449147063794743 28.613259590040926 chr4 191154276 320520561 1.676763751808513 21.492300898242554 chr5 180915260 354352790 1.9586672235387994 23.20692170111026 chr6 171115067 603899991 3.529204070615243 41.09561122197188 chr7 159138663 378419283 2.3779217184952723 28.318673605151307 chr8 146364022 248499453 1.6978178763084277 20.033376560180482 chr9 141213431 303633948 2.1501775422480884 24.575637647933632 chr10 135534747 317849711 2.345152944432766 25.471497992768708 chr11 135006516 334689630 2.4790627883471936 25.437679617822933 chr12 133851895 390602715 2.918170975465084 28.181596834987207 chr13 115169878 148413352 1.2886472971691434 19.60700906146394 chr14 107349540 239790186 2.2337327761255428 25.122523629313005 chr15 102531392 259403862 2.529994540598844 26.689580942511913 chr16 90354753 233816932 2.587765714992326 26.377993323314275 chr17 81195210 285653207 3.5181041714160233 30.45971668525676 chr18 78077248 124624656 1.5961712175101253 21.546595924652898 chr19 59128983 269025465 4.549807071770539 36.32602680855341 chr20 63025520 183520562 2.911845265219549 33.07099902247351 chr21 48129895 72887117 1.5143834616717946 18.930947307817615 chr22 51304566 125519253 2.446551306953849 25.042856412387888 chrMT 16571 165534 9.989379035664715 13.925573181971277 chrX 155270560 173495937 1.117378188112415 13.94878762500153 chrY 59373566 13794627 0.23233617128538314 4.229769051399208