BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961008.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 = 391,567,662 number of mapped reads = 383,724,637 (98%) number of supplementary alignments = 825,645 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 192,107,293 number of mapped paired reads (second in pair) = 191,617,344 number of mapped paired reads (both in pair) = 382,649,306 number of mapped paired reads (singletons) = 1,075,331 number of mapped bases = 37,454,102,649 bp number of sequenced bases = 37,442,571,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,396,304 duplication rate = 12.11% >>>>>>> Insert size mean insert size = 16,085.9676 std insert size = 1,222,395.888 median insert size = 124 >>>>>>> Mapping quality mean mapping quality = 53.5888 >>>>>>> ACTG content number of A's = 11,094,520,793 bp (29.63%) number of C's = 7,604,695,418 bp (20.31%) number of T's = 11,039,907,373 bp (29.48%) number of G's = 7,682,625,477 bp (20.52%) number of N's = 20,822,081 bp (0.06%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 206,852,992 number of insertions = 3,845,604 mapped reads with insertion percentage = 0.97% number of deletions = 4,520,440 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 12.0988X std coverageData = 142.9665X There is a 91.23% of reference with a coverageData >= 1X There is a 90.56% of reference with a coverageData >= 2X There is a 89.03% of reference with a coverageData >= 3X There is a 86.95% of reference with a coverageData >= 4X There is a 83.76% of reference with a coverageData >= 5X There is a 79.9% of reference with a coverageData >= 6X There is a 75.1% of reference with a coverageData >= 7X There is a 69.84% of reference with a coverageData >= 8X There is a 64.06% of reference with a coverageData >= 9X There is a 58.17% of reference with a coverageData >= 10X There is a 52.19% of reference with a coverageData >= 11X There is a 46.39% of reference with a coverageData >= 12X There is a 40.81% of reference with a coverageData >= 13X There is a 35.58% of reference with a coverageData >= 14X There is a 30.73% of reference with a coverageData >= 15X There is a 26.33% of reference with a coverageData >= 16X There is a 22.36% of reference with a coverageData >= 17X There is a 18.85% of reference with a coverageData >= 18X There is a 15.78% of reference with a coverageData >= 19X There is a 13.12% of reference with a coverageData >= 20X There is a 10.84% of reference with a coverageData >= 21X There is a 8.91% of reference with a coverageData >= 22X There is a 7.29% of reference with a coverageData >= 23X There is a 5.94% of reference with a coverageData >= 24X There is a 4.83% of reference with a coverageData >= 25X There is a 3.92% of reference with a coverageData >= 26X There is a 3.17% of reference with a coverageData >= 27X There is a 2.57% of reference with a coverageData >= 28X There is a 2.08% of reference with a coverageData >= 29X There is a 1.69% of reference with a coverageData >= 30X There is a 1.38% of reference with a coverageData >= 31X There is a 1.13% of reference with a coverageData >= 32X There is a 0.93% of reference with a coverageData >= 33X There is a 0.77% of reference with a coverageData >= 34X There is a 0.65% of reference with a coverageData >= 35X There is a 0.55% of reference with a coverageData >= 36X There is a 0.47% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.32% of reference with a coverageData >= 40X There is a 0.29% of reference with a coverageData >= 41X There is a 0.26% of reference with a coverageData >= 42X There is a 0.24% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3233618237 12.973360804585518 343.7738771135807 chr2 243199373 3868180633 15.90538900361392 83.63324044407129 chr3 198022430 2395831652 12.098789273518156 42.04985927767249 chr4 191154276 1995290623 10.438116607969576 117.72771451653945 chr5 180915260 1966856524 10.871700507740474 13.263672578771274 chr6 171115067 2223569296 12.994585076485404 41.66666520728562 chr7 159138663 1927921351 12.114726331463524 88.4774559475785 chr8 146364022 2099092300 14.341586622974873 134.53208403534026 chr9 141213431 1891895102 13.397416156541087 95.56073150523439 chr10 135534747 1653617277 12.200688853611835 352.0114540471092 chr11 135006516 1671626050 12.381817556124476 54.822034477040646 chr12 133851895 1883436395 14.071047668021436 13.06876780978153 chr13 115169878 1016357036 8.824851199373503 7.7313101663800055 chr14 107349540 745619672 6.945718370102005 12.403893556811484 chr15 102531392 947194928 9.238096835747632 7.386640569578602 chr16 90354753 1081934355 11.974293759621036 134.7573104648295 chr17 81195210 909546922 11.201977579711906 37.000013427253585 chr18 78077248 1145654840 14.673350679573133 127.30365597334067 chr19 59128983 780938013 13.207364195660189 173.20438685922196 chr20 63025520 793026683 12.582628163956441 37.713267058283385 chr21 48129895 461651318 9.5917790387866 64.777783507916 chr22 51304566 520170024 10.138864131508296 11.457493372236366 chrMT 16571 17623348 1063.50540100175 182.4556053974808 chrX 155270560 2101385806 13.533704045377307 42.70050173887004 chrY 59373566 122064264 2.055868835636384 125.9456500634451