BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124837.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 830,295,530 number of mapped reads = 819,936,146 (98.75%) number of supplementary alignments = 7,063,399 (0.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 412,656,254 number of mapped paired reads (second in pair) = 407,279,892 number of mapped paired reads (both in pair) = 813,861,092 number of mapped paired reads (singletons) = 6,075,054 number of mapped bases = 120,337,437,439 bp number of sequenced bases = 120,296,882,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,405,605 duplication rate = 22.82% >>>>>>> Insert size mean insert size = 54,249.1803 std insert size = 2,269,239.767 median insert size = 295 >>>>>>> Mapping quality mean mapping quality = 54.5147 >>>>>>> ACTG content number of A's = 35,499,371,323 bp (29.51%) number of C's = 24,604,111,849 bp (20.45%) number of T's = 35,559,821,241 bp (29.56%) number of G's = 24,630,299,627 bp (20.47%) number of N's = 3,278,066 bp (0%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 865,428,280 number of insertions = 12,172,971 mapped reads with insertion percentage = 1.4% number of deletions = 13,600,850 mapped reads with deletion percentage = 1.58% homopolymer indels = 41.66% >>>>>>> Coverage mean coverageData = 38.8725X std coverageData = 280.6769X There is a 92.34% of reference with a coverageData >= 1X There is a 92.3% of reference with a coverageData >= 2X There is a 92.26% of reference with a coverageData >= 3X There is a 92.21% of reference with a coverageData >= 4X There is a 92.16% of reference with a coverageData >= 5X There is a 92.11% of reference with a coverageData >= 6X There is a 92.04% of reference with a coverageData >= 7X There is a 91.97% of reference with a coverageData >= 8X There is a 91.88% of reference with a coverageData >= 9X There is a 91.77% of reference with a coverageData >= 10X There is a 91.65% of reference with a coverageData >= 11X There is a 91.49% of reference with a coverageData >= 12X There is a 91.3% of reference with a coverageData >= 13X There is a 91.07% of reference with a coverageData >= 14X There is a 90.78% of reference with a coverageData >= 15X There is a 90.44% of reference with a coverageData >= 16X There is a 90.02% of reference with a coverageData >= 17X There is a 89.51% of reference with a coverageData >= 18X There is a 88.91% of reference with a coverageData >= 19X There is a 88.2% of reference with a coverageData >= 20X There is a 87.37% of reference with a coverageData >= 21X There is a 86.41% of reference with a coverageData >= 22X There is a 85.31% of reference with a coverageData >= 23X There is a 84.07% of reference with a coverageData >= 24X There is a 82.67% of reference with a coverageData >= 25X There is a 81.12% of reference with a coverageData >= 26X There is a 79.4% of reference with a coverageData >= 27X There is a 77.54% of reference with a coverageData >= 28X There is a 75.51% of reference with a coverageData >= 29X There is a 73.34% of reference with a coverageData >= 30X There is a 71.03% of reference with a coverageData >= 31X There is a 68.59% of reference with a coverageData >= 32X There is a 66.03% of reference with a coverageData >= 33X There is a 63.36% of reference with a coverageData >= 34X There is a 60.61% of reference with a coverageData >= 35X There is a 57.79% of reference with a coverageData >= 36X There is a 54.93% of reference with a coverageData >= 37X There is a 52.03% of reference with a coverageData >= 38X There is a 49.13% of reference with a coverageData >= 39X There is a 46.23% of reference with a coverageData >= 40X There is a 43.36% of reference with a coverageData >= 41X There is a 40.54% of reference with a coverageData >= 42X There is a 37.79% of reference with a coverageData >= 43X There is a 35.11% of reference with a coverageData >= 44X There is a 32.52% of reference with a coverageData >= 45X There is a 30.04% of reference with a coverageData >= 46X There is a 27.67% of reference with a coverageData >= 47X There is a 25.41% of reference with a coverageData >= 48X There is a 23.27% of reference with a coverageData >= 49X There is a 21.26% of reference with a coverageData >= 50X There is a 19.38% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 10413318560 41.77850598013154 681.6565757770467 chr2 243199373 10334538725 42.49410102303183 270.5948006090517 chr3 198022430 8632773086 43.594925514246036 21.05078348014917 chr4 191154276 7433902732 38.88954454777669 186.68133280431306 chr5 180915260 7456100824 41.21322227876189 35.678004549578596 chr6 171115067 6943172004 40.576041173510454 110.44591505171141 chr7 159138663 7831595933 49.21240247569505 184.51436726569082 chr8 146364022 7312616832 49.96184671667468 298.44566191072767 chr9 141213431 4928938720 34.904177917750616 330.6606057333941 chr10 135534747 5531064607 40.809200071772004 455.360734912605 chr11 135006516 4920079912 36.44327738966318 97.97537896416763 chr12 133851895 5702371162 42.60209511415584 190.08424556392072 chr13 115169878 3613893949 31.378811992837225 18.57892920339238 chr14 107349540 3970030180 36.9822747260957 24.703294919927664 chr15 102531392 3304376491 32.227949182626915 107.4523407727949 chr16 90354753 3478007090 38.492796167568514 113.84764142084055 chr17 81195210 2758947016 33.9791844371115 138.41174669621293 chr18 78077248 2649694458 33.93683212297647 306.87312353631256 chr19 59128983 2038143507 34.46944972823226 295.9015905162771 chr20 63025520 2575522905 40.8647624803413 67.55319006017193 chr21 48129895 1491052177 30.979751295946105 124.59628483422391 chr22 51304566 1166020152 22.727414787993723 101.19466406452679 chrMT 16571 425837276 25697.741596765434 2821.8217249881322 chrX 155270560 4333551700 27.909680366967184 49.840356652110046 chrY 59373566 1091887441 18.390127367455072 239.19478552708736