BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504703.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 498,300,510 number of mapped reads = 451,655,631 (90.64%) number of supplementary alignments = 2,289,623 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 226,795,588 number of mapped paired reads (second in pair) = 224,860,043 number of mapped paired reads (both in pair) = 446,268,380 number of mapped paired reads (singletons) = 5,387,251 number of mapped bases = 44,362,531,217 bp number of sequenced bases = 44,353,183,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,941,344 duplication rate = 23.36% >>>>>>> Insert size mean insert size = 42,949.9933 std insert size = 1,932,946.2089 median insert size = 410 >>>>>>> Mapping quality mean mapping quality = 53.808 >>>>>>> ACTG content number of A's = 11,746,503,168 bp (26.48%) number of C's = 10,324,609,297 bp (23.28%) number of T's = 11,765,913,513 bp (26.53%) number of G's = 10,493,343,921 bp (23.66%) number of N's = 22,813,194 bp (0.05%) GC percentage = 46.94% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 311,357,709 number of insertions = 3,033,525 mapped reads with insertion percentage = 0.66% number of deletions = 3,823,273 mapped reads with deletion percentage = 0.83% homopolymer indels = 41.12% >>>>>>> Coverage mean coverageData = 14.3304X std coverageData = 34.0863X There is a 76.15% of reference with a coverageData >= 1X There is a 68.48% of reference with a coverageData >= 2X There is a 62.16% of reference with a coverageData >= 3X There is a 57.05% of reference with a coverageData >= 4X There is a 52.61% of reference with a coverageData >= 5X There is a 48.71% of reference with a coverageData >= 6X There is a 45.24% of reference with a coverageData >= 7X There is a 42.13% of reference with a coverageData >= 8X There is a 39.33% of reference with a coverageData >= 9X There is a 36.79% of reference with a coverageData >= 10X There is a 34.48% of reference with a coverageData >= 11X There is a 32.38% of reference with a coverageData >= 12X There is a 30.46% of reference with a coverageData >= 13X There is a 28.7% of reference with a coverageData >= 14X There is a 27.08% of reference with a coverageData >= 15X There is a 25.59% of reference with a coverageData >= 16X There is a 24.22% of reference with a coverageData >= 17X There is a 22.95% of reference with a coverageData >= 18X There is a 21.78% of reference with a coverageData >= 19X There is a 20.68% of reference with a coverageData >= 20X There is a 19.67% of reference with a coverageData >= 21X There is a 18.72% of reference with a coverageData >= 22X There is a 17.84% of reference with a coverageData >= 23X There is a 17.02% of reference with a coverageData >= 24X There is a 16.25% of reference with a coverageData >= 25X There is a 15.53% of reference with a coverageData >= 26X There is a 14.85% of reference with a coverageData >= 27X There is a 14.22% of reference with a coverageData >= 28X There is a 13.62% of reference with a coverageData >= 29X There is a 13.06% of reference with a coverageData >= 30X There is a 12.53% of reference with a coverageData >= 31X There is a 12.04% of reference with a coverageData >= 32X There is a 11.56% of reference with a coverageData >= 33X There is a 11.12% of reference with a coverageData >= 34X There is a 10.7% of reference with a coverageData >= 35X There is a 10.3% of reference with a coverageData >= 36X There is a 9.92% of reference with a coverageData >= 37X There is a 9.56% of reference with a coverageData >= 38X There is a 9.22% of reference with a coverageData >= 39X There is a 8.9% of reference with a coverageData >= 40X There is a 8.59% of reference with a coverageData >= 41X There is a 8.3% of reference with a coverageData >= 42X There is a 8.02% of reference with a coverageData >= 43X There is a 7.75% of reference with a coverageData >= 44X There is a 7.5% of reference with a coverageData >= 45X There is a 7.25% of reference with a coverageData >= 46X There is a 7.02% of reference with a coverageData >= 47X There is a 6.8% of reference with a coverageData >= 48X There is a 6.58% of reference with a coverageData >= 49X There is a 6.38% of reference with a coverageData >= 50X There is a 6.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3655175812 14.664660803392742 31.208234902372602 chr2 243199373 3029942741 12.45867825901015 23.5371823984242 chr3 198022430 2585300301 13.055593252744146 24.76458215939708 chr4 191154276 1905621485 9.96902358072283 17.818409488582986 chr5 180915260 2900108356 16.030203068552648 30.94283106431398 chr6 171115067 1340371531 7.833159022752801 15.637949679961164 chr7 159138663 2272091953 14.277435226410065 24.572284041755292 chr8 146364022 2494080722 17.040258172189336 33.54845984697935 chr9 141213431 1061995937 7.5205023309716195 27.87138721457229 chr10 135534747 3014830279 22.243965814906492 35.518735558872066 chr11 135006516 2659008267 19.695406901693545 35.96363504090559 chr12 133851895 2018921296 15.083247764254663 35.55199592189478 chr13 115169878 620762202 5.389970127432105 10.925828335516876 chr14 107349540 1280936016 11.9323847684862 23.519222609664872 chr15 102531392 1574211410 15.353457895119575 29.951578780450276 chr16 90354753 2229144940 24.671031307008278 41.549274025456334 chr17 81195210 1734157707 21.35788191199949 40.54473289983247 chr18 78077248 691382315 8.855106099538753 98.40985057568254 chr19 59128983 1907094474 32.2531249015394 60.18799481121202 chr20 63025520 1365332956 21.663176376807364 35.40421576460998 chr21 48129895 565987188 11.759576620726058 25.360634107580463 chr22 51304566 730121993 14.23113087049601 29.459111627847147 chrMT 16571 200195 12.081045199444814 17.25076407594333 chrX 155270560 2642399105 17.018030365833678 28.38905068039316 chrY 59373566 83352036 1.4038576695898644 48.555626648137405