BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365375.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 659,386,010 number of mapped reads = 630,780,989 (95.66%) number of supplementary alignments = 4,360,243 (0.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 315,053,231 number of mapped paired reads (second in pair) = 315,727,758 number of mapped paired reads (both in pair) = 629,277,342 number of mapped paired reads (singletons) = 1,503,647 number of mapped bases = 73,784,173,439 bp number of sequenced bases = 73,757,419,080 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 376,487,016 duplication rate = 39.35% >>>>>>> Insert size mean insert size = 61,166.2987 std insert size = 2,403,565.9984 median insert size = 135 >>>>>>> Mapping quality mean mapping quality = 53.896 >>>>>>> ACTG content number of A's = 21,888,552,623 bp (29.68%) number of C's = 14,988,240,469 bp (20.32%) number of T's = 21,230,398,218 bp (28.78%) number of G's = 15,646,326,079 bp (21.21%) number of N's = 3,901,691 bp (0.01%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 350,517,526 number of insertions = 23,917,806 mapped reads with insertion percentage = 3.68% number of deletions = 12,038,088 mapped reads with deletion percentage = 1.85% homopolymer indels = 49.82% >>>>>>> Coverage mean coverageData = 23.8345X std coverageData = 324.2984X There is a 88.75% of reference with a coverageData >= 1X There is a 87.38% of reference with a coverageData >= 2X There is a 85.07% of reference with a coverageData >= 3X There is a 83.31% of reference with a coverageData >= 4X There is a 80.94% of reference with a coverageData >= 5X There is a 78.89% of reference with a coverageData >= 6X There is a 76.44% of reference with a coverageData >= 7X There is a 74.21% of reference with a coverageData >= 8X There is a 71.72% of reference with a coverageData >= 9X There is a 69.41% of reference with a coverageData >= 10X There is a 66.92% of reference with a coverageData >= 11X There is a 64.58% of reference with a coverageData >= 12X There is a 62.13% of reference with a coverageData >= 13X There is a 59.8% of reference with a coverageData >= 14X There is a 57.41% of reference with a coverageData >= 15X There is a 55.15% of reference with a coverageData >= 16X There is a 52.85% of reference with a coverageData >= 17X There is a 50.67% of reference with a coverageData >= 18X There is a 48.49% of reference with a coverageData >= 19X There is a 46.41% of reference with a coverageData >= 20X There is a 44.34% of reference with a coverageData >= 21X There is a 42.38% of reference with a coverageData >= 22X There is a 40.44% of reference with a coverageData >= 23X There is a 38.6% of reference with a coverageData >= 24X There is a 36.8% of reference with a coverageData >= 25X There is a 35.08% of reference with a coverageData >= 26X There is a 33.4% of reference with a coverageData >= 27X There is a 31.82% of reference with a coverageData >= 28X There is a 30.27% of reference with a coverageData >= 29X There is a 28.8% of reference with a coverageData >= 30X There is a 27.38% of reference with a coverageData >= 31X There is a 26.03% of reference with a coverageData >= 32X There is a 24.72% of reference with a coverageData >= 33X There is a 23.49% of reference with a coverageData >= 34X There is a 22.3% of reference with a coverageData >= 35X There is a 21.17% of reference with a coverageData >= 36X There is a 20.08% of reference with a coverageData >= 37X There is a 19.05% of reference with a coverageData >= 38X There is a 18.06% of reference with a coverageData >= 39X There is a 17.13% of reference with a coverageData >= 40X There is a 16.23% of reference with a coverageData >= 41X There is a 15.38% of reference with a coverageData >= 42X There is a 14.57% of reference with a coverageData >= 43X There is a 13.81% of reference with a coverageData >= 44X There is a 13.07% of reference with a coverageData >= 45X There is a 12.38% of reference with a coverageData >= 46X There is a 11.72% of reference with a coverageData >= 47X There is a 11.1% of reference with a coverageData >= 48X There is a 10.51% of reference with a coverageData >= 49X There is a 9.95% of reference with a coverageData >= 50X There is a 9.42% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6378797771 25.59190322338254 919.5790085207869 chr2 243199373 6364238223 26.168810159720273 190.44672515742423 chr3 198022430 5136031842 25.936616584293002 47.314466996540204 chr4 191154276 4943454556 25.86107232045387 107.54208366704623 chr5 180915260 4456842295 24.634971615993035 30.846046900557173 chr6 171115067 4320361658 25.24828312167274 117.86417395490626 chr7 159138663 4184832651 26.29676894420057 230.5543011097243 chr8 146364022 3550365094 24.257088903993086 91.04033088218056 chr9 141213431 3105577353 21.99208199254078 294.9102311044843 chr10 135534747 3815473038 28.15125362649624 559.1328594160647 chr11 135006516 3493759530 25.87845115564644 188.28945186965305 chr12 133851895 3088732221 23.075745180895645 36.77471194448275 chr13 115169878 2468729175 21.435545629387573 22.121346040677803 chr14 107349540 2322756316 21.63731969415053 31.43763878952955 chr15 102531392 2030781575 19.806437183648107 24.000874955942134 chr16 90354753 2151223408 23.808635811333577 87.76122506958438 chr17 81195210 2004951837 24.69298172884829 147.64896174858882 chr18 78077248 2089493510 26.761874470780526 341.20741761624936 chr19 59128983 1446921409 24.47059522400377 486.8948413159773 chr20 63025520 1620186477 25.706832359336346 47.9878721958842 chr21 48129895 1035600436 21.516781534636632 99.11246328065987 chr22 51304566 905171699 17.6431021558588 83.60952510328764 chrMT 16571 71155188 4293.958602377647 893.856282738113 chrX 155270560 2071605941 13.341910668706289 74.60089690110115 chrY 59373566 727130236 12.246699751872745 242.49024233084495