BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231746.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,644,523 number of mapped reads = 4,374,850 (94.19%) number of supplementary alignments = 48,199 (1.04%) number of secondary alignments = 0 number of mapped bases = 300,229,329 bp number of sequenced bases = 300,124,154 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 741,195 duplication rate = 8.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4994 >>>>>>> ACTG content number of A's = 77,518,223 bp (25.83%) number of C's = 55,432,296 bp (18.47%) number of T's = 83,398,317 bp (27.79%) number of G's = 83,709,785 bp (27.89%) number of N's = 65,533 bp (0.02%) GC percentage = 46.36% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,915,769 number of insertions = 20,442 mapped reads with insertion percentage = 0.46% number of deletions = 64,805 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.097X std coverageData = 43.2177X There is a 4.39% of reference with a coverageData >= 1X There is a 2.17% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 21815879 0.08752587621436658 1.293476488477133 chr2 243199373 41507206 0.17067151731513716 154.16818223449928 chr3 198022430 23927657 0.12083306421398829 0.6071763076473341 chr4 191154276 4764084 0.024922717397124823 0.31633655048732523 chr5 180915260 16564618 0.09156009283020128 0.5415730865015214 chr6 171115067 20198789 0.11804214178287409 0.780630545329885 chr7 159138663 11831188 0.07434515143563825 0.8786093336834923 chr8 146364022 11695545 0.07990723977235334 0.7942718792601988 chr9 141213431 2924847 0.0207122437241823 0.5413551432137798 chr10 135534747 19485399 0.14376681575242103 0.9126552247512733 chr11 135006516 12658363 0.09376112631482172 1.061699179217973 chr12 133851895 14105694 0.1053828487075211 0.5682588812004814 chr13 115169878 852668 0.007403567797475656 0.13964941701413505 chr14 107349540 7932593 0.07389498827847796 0.60198719110768 chr15 102531392 15527368 0.15144013649985363 0.6909492930530791 chr16 90354753 7558320 0.08365160380660883 0.5408367401702031 chr17 81195210 7563509 0.09315215762112075 0.6876885547758753 chr18 78077248 9401815 0.120416833851521 1.278009079919994 chr19 59128983 13372905 0.226164975643163 1.0719107202492213 chr20 63025520 10130243 0.16073239855855215 0.7267109080773018 chr21 48129895 6634818 0.13785232650102394 0.7002434317203676 chr22 51304566 5512702 0.10745051424857585 0.5887195342657751 chrMT 16571 31122 1.8781002956973025 2.6337073670772404 chrX 155270560 13520450 0.08707671306138137 0.5729304377275136 chrY 59373566 711547 0.011984238911976417 0.26203755970242576