BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472517.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,398,428 number of mapped reads = 16,242,854 (99.05%) number of supplementary alignments = 68,014 (0.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,141,194 number of mapped paired reads (second in pair) = 8,101,660 number of mapped paired reads (both in pair) = 16,162,800 number of mapped paired reads (singletons) = 80,054 number of mapped bases = 1,596,542,967 bp number of sequenced bases = 1,596,364,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,192,754 duplication rate = 46.11% >>>>>>> Insert size mean insert size = 32,717.4388 std insert size = 1,790,256.0028 median insert size = 223 >>>>>>> Mapping quality mean mapping quality = 55.0364 >>>>>>> ACTG content number of A's = 434,122,642 bp (27.19%) number of C's = 366,534,419 bp (22.96%) number of T's = 431,374,354 bp (27.02%) number of G's = 364,084,459 bp (22.81%) number of N's = 248,451 bp (0.02%) GC percentage = 45.77% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 9,020,417 number of insertions = 85,046 mapped reads with insertion percentage = 0.52% number of deletions = 76,577 mapped reads with deletion percentage = 0.47% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 0.5157X std coverageData = 19.0209X There is a 5.13% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.7% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 158976197 0.6378166536243053 26.036883609823832 chr2 243199373 121644439 0.5001840156882312 17.66934393455895 chr3 198022430 180239827 0.9101990466433525 21.202598902354787 chr4 191154276 46505585 0.2432882275675591 9.357730449214678 chr5 180915260 89818037 0.4964646818626577 16.672470048491384 chr6 171115067 104743229 0.6121216023601241 17.643476374421095 chr7 159138663 92284713 0.5799012713836863 26.478056512963295 chr8 146364022 74928887 0.5119351461932359 18.352158494147385 chr9 141213431 75233999 0.5327680126970359 13.12100339629067 chr10 135534747 37835797 0.2791593878136652 10.256468187932464 chr11 135006516 69480486 0.5146454264474168 16.97387684312554 chr12 133851895 93270053 0.6968153345905189 29.231785961873776 chr13 115169878 36889576 0.3203057660615044 12.218771010999424 chr14 107349540 35434755 0.33008762776254097 12.183236065958338 chr15 102531392 45009476 0.4389823947772015 14.124310464864722 chr16 90354753 53202607 0.5888191294153613 15.554223150179729 chr17 81195210 52685426 0.6488735727144496 20.22590016852792 chr18 78077248 31361873 0.40167748996481023 17.344330024957266 chr19 59128983 36008033 0.6089743332808548 16.245224818712927 chr20 63025520 35351315 0.5609047731775954 18.2832616367762 chr21 48129895 5897122 0.12252513744316293 4.501631402489999 chr22 51304566 23962523 0.46706414006114 17.986461617007198 chrMT 16571 1269 0.07657956671293223 0.29517681867664997 chrX 155270560 85650737 0.5516225162065493 26.331847131424833 chrY 59373566 10127006 0.17056422044786732 17.860430915595646