BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617600.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 47,369,174 number of mapped reads = 46,431,485 (98.02%) number of supplementary alignments = 757,913 (1.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,461,735 number of mapped paired reads (second in pair) = 22,969,750 number of mapped paired reads (both in pair) = 45,812,488 number of mapped paired reads (singletons) = 618,997 number of mapped bases = 6,242,282,168 bp number of sequenced bases = 6,237,991,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,659,724 duplication rate = 22.08% >>>>>>> Insert size mean insert size = 107,816.5379 std insert size = 3,157,814.8347 median insert size = 281 >>>>>>> Mapping quality mean mapping quality = 53.682 >>>>>>> ACTG content number of A's = 1,804,123,167 bp (28.92%) number of C's = 1,186,955,176 bp (19.03%) number of T's = 1,860,226,448 bp (29.82%) number of G's = 1,386,430,949 bp (22.23%) number of N's = 255,757 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.012 number of mismatches = 71,849,099 number of insertions = 1,030,929 mapped reads with insertion percentage = 2.09% number of deletions = 2,194,642 mapped reads with deletion percentage = 4.54% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 2.0164X std coverageData = 19.6945X There is a 46.48% of reference with a coverageData >= 1X There is a 33.51% of reference with a coverageData >= 2X There is a 24.5% of reference with a coverageData >= 3X There is a 18.51% of reference with a coverageData >= 4X There is a 14.09% of reference with a coverageData >= 5X There is a 10.9% of reference with a coverageData >= 6X There is a 8.5% of reference with a coverageData >= 7X There is a 6.69% of reference with a coverageData >= 8X There is a 5.3% of reference with a coverageData >= 9X There is a 4.23% of reference with a coverageData >= 10X There is a 3.4% of reference with a coverageData >= 11X There is a 2.74% of reference with a coverageData >= 12X There is a 2.23% of reference with a coverageData >= 13X There is a 1.82% of reference with a coverageData >= 14X There is a 1.49% of reference with a coverageData >= 15X There is a 1.23% of reference with a coverageData >= 16X There is a 1.02% of reference with a coverageData >= 17X There is a 0.85% of reference with a coverageData >= 18X There is a 0.71% of reference with a coverageData >= 19X There is a 0.6% of reference with a coverageData >= 20X There is a 0.5% of reference with a coverageData >= 21X There is a 0.43% of reference with a coverageData >= 22X There is a 0.36% of reference with a coverageData >= 23X There is a 0.31% of reference with a coverageData >= 24X There is a 0.27% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.17% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 507339840 2.0354606859735767 18.02518829308476 chr2 243199373 588708134 2.4206811339106538 22.711316158691073 chr3 198022430 446084549 2.252697075780759 4.266242383074419 chr4 191154276 431165765 2.2555904791792365 17.50635644180317 chr5 180915260 327385194 1.809605193061105 3.8057940522194995 chr6 171115067 389959850 2.278933450085959 11.002526158556362 chr7 159138663 343043767 2.1556280575261586 20.284709324339158 chr8 146364022 330048517 2.2549839263094316 5.857155720718716 chr9 141213431 283473497 2.0074117241723273 35.74329019827541 chr10 135534747 320459603 2.364409202018136 57.12499521161629 chr11 135006516 301133263 2.2305091037235565 10.897255706577116 chr12 133851895 285543513 2.133279569930631 7.143878121136836 chr13 115169878 156266147 1.3568317490099278 2.9270627994775023 chr14 107349540 195581503 1.821912818629684 4.021348019429998 chr15 102531392 179911501 1.7546967566772136 4.466840086860051 chr16 90354753 197883658 2.190074693690989 20.321202320720136 chr17 81195210 150811775 1.8573974376074647 20.77417257423662 chr18 78077248 179305152 2.296509631077161 24.50248407044812 chr19 59128983 91105558 1.5407935901755658 10.828684212320079 chr20 63025520 138392799 2.1958216132131874 6.227752551361472 chr21 48129895 80816102 1.6791248349908097 9.166739480943939 chr22 51304566 35844020 0.6986516560728727 2.6823159310119857 chrMT 16571 953703 57.55253153098787 29.212128782149424 chrX 155270560 207951694 1.3392860436646845 4.661092930780835 chrY 59373566 73113064 1.2314076604393276 29.334838594514018