BamQC report ----------------------------------- >>>>>>> Input bam file = SRR16328247.sorted.bam outfile = /mainsd2/zhouyj/SRP341378/SRP341378.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 = 208,339,152 number of mapped reads = 197,752,432 (94.92%) number of supplementary alignments = 11,200,744 (5.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 101,280,509 number of mapped paired reads (second in pair) = 96,471,923 number of mapped paired reads (both in pair) = 192,106,212 number of mapped paired reads (singletons) = 5,646,220 number of mapped bases = 27,148,501,359 bp number of sequenced bases = 27,084,889,522 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 92,245,770 duplication rate = 35.12% >>>>>>> Insert size mean insert size = 332,612.9414 std insert size = 5,697,166.0953 median insert size = 321 >>>>>>> Mapping quality mean mapping quality = 52.6222 >>>>>>> ACTG content number of A's = 7,719,591,047 bp (28.5%) number of C's = 5,783,320,997 bp (21.35%) number of T's = 7,711,261,051 bp (28.47%) number of G's = 5,868,877,210 bp (21.67%) number of N's = 1,839,217 bp (0.01%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.0143 number of mismatches = 364,574,632 number of insertions = 7,374,749 mapped reads with insertion percentage = 3.38% number of deletions = 22,295,793 mapped reads with deletion percentage = 10.55% homopolymer indels = 47.16% >>>>>>> Coverage mean coverageData = 8.7698X std coverageData = 124.5522X There is a 89.03% of reference with a coverageData >= 1X There is a 83.72% of reference with a coverageData >= 2X There is a 76.74% of reference with a coverageData >= 3X There is a 68.99% of reference with a coverageData >= 4X There is a 61.04% of reference with a coverageData >= 5X There is a 53.41% of reference with a coverageData >= 6X There is a 46.35% of reference with a coverageData >= 7X There is a 40.04% of reference with a coverageData >= 8X There is a 34.48% of reference with a coverageData >= 9X There is a 29.68% of reference with a coverageData >= 10X There is a 25.56% of reference with a coverageData >= 11X There is a 22.05% of reference with a coverageData >= 12X There is a 19.07% of reference with a coverageData >= 13X There is a 16.54% of reference with a coverageData >= 14X There is a 14.4% of reference with a coverageData >= 15X There is a 12.58% of reference with a coverageData >= 16X There is a 11.03% of reference with a coverageData >= 17X There is a 9.7% of reference with a coverageData >= 18X There is a 8.57% of reference with a coverageData >= 19X There is a 7.6% of reference with a coverageData >= 20X There is a 6.77% of reference with a coverageData >= 21X There is a 6.05% of reference with a coverageData >= 22X There is a 5.42% of reference with a coverageData >= 23X There is a 4.87% of reference with a coverageData >= 24X There is a 4.4% of reference with a coverageData >= 25X There is a 3.98% of reference with a coverageData >= 26X There is a 3.61% of reference with a coverageData >= 27X There is a 3.28% of reference with a coverageData >= 28X There is a 2.99% of reference with a coverageData >= 29X There is a 2.74% of reference with a coverageData >= 30X There is a 2.51% of reference with a coverageData >= 31X There is a 2.31% of reference with a coverageData >= 32X There is a 2.12% of reference with a coverageData >= 33X There is a 1.96% of reference with a coverageData >= 34X There is a 1.81% of reference with a coverageData >= 35X There is a 1.67% of reference with a coverageData >= 36X There is a 1.55% of reference with a coverageData >= 37X There is a 1.44% of reference with a coverageData >= 38X There is a 1.34% of reference with a coverageData >= 39X There is a 1.25% of reference with a coverageData >= 40X There is a 1.16% of reference with a coverageData >= 41X There is a 1.09% of reference with a coverageData >= 42X There is a 1.02% of reference with a coverageData >= 43X There is a 0.95% of reference with a coverageData >= 44X There is a 0.89% of reference with a coverageData >= 45X There is a 0.84% of reference with a coverageData >= 46X There is a 0.79% of reference with a coverageData >= 47X There is a 0.74% of reference with a coverageData >= 48X There is a 0.7% of reference with a coverageData >= 49X There is a 0.66% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2172768451 8.71720376175111 144.37751880136827 chr2 243199373 2315111567 9.519397761769723 268.17632535366624 chr3 198022430 1701558656 8.592757174023165 14.663727354778146 chr4 191154276 1796620450 9.39879812052962 176.31915259542873 chr5 180915260 1541682145 8.52157051317838 15.04624785573498 chr6 171115067 1470673306 8.594645297950297 26.846856645937933 chr7 159138663 1438502044 9.039299544699581 56.47665667387546 chr8 146364022 1624859999 11.101498693442572 166.2374485856341 chr9 141213431 1125077894 7.967215908804029 85.33230535910081 chr10 135534747 1520870557 11.221259423607439 193.32528265227526 chr11 135006516 1186983943 8.792049288939506 29.963741244168865 chr12 133851895 1203377965 8.990369280913058 37.08214528743152 chr13 115169878 795052216 6.903299975710663 20.76171700758516 chr14 107349540 800576550 7.457661672327613 19.669616916371304 chr15 102531392 753285660 7.346878310205717 11.966080836130121 chr16 90354753 940463484 10.408566818836858 91.66725537609521 chr17 81195210 979268167 12.060664255933323 51.69741012676317 chr18 78077248 681375039 8.726934625052358 70.70731198578837 chr19 59128983 643113387 10.876449320970057 107.62014684966904 chr20 63025520 572775040 9.087985946010441 49.650821394225034 chr21 48129895 388878810 8.079776820622609 92.9498057419501 chr22 51304566 351711932 6.855372911642991 18.429666697638105 chrMT 16571 209715989 12655.602498340475 7524.3350751406615 chrX 155270560 732291290 4.716227532121994 15.52134989509929 chrY 59373566 201906818 3.4006180123996597 177.00211785675535