BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751173.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 4,096,241 number of mapped reads = 3,471,326 (84.74%) number of supplementary alignments = 166,522 (4.07%) number of secondary alignments = 0 number of mapped bases = 341,138,830 bp number of sequenced bases = 341,028,126 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,159 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0932 >>>>>>> ACTG content number of A's = 100,334,330 bp (29.42%) number of C's = 70,158,653 bp (20.57%) number of T's = 100,878,687 bp (29.58%) number of G's = 69,654,649 bp (20.42%) number of N's = 1,807 bp (0%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 1,352,276 number of insertions = 128,811 mapped reads with insertion percentage = 3.61% number of deletions = 50,007 mapped reads with deletion percentage = 1.41% homopolymer indels = 50.13% >>>>>>> Coverage mean coverageData = 0.1102X std coverageData = 1.1839X There is a 8.84% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% of reference with a coverageData >= 13X There is a 0% 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 41216299 0.1653608678471457 3.3545452094220947 chr2 243199373 26262555 0.10798775784672768 0.5195863682523263 chr3 198022430 19051796 0.09621029294509718 0.42815937843607715 chr4 191154276 16255638 0.08503936370222762 0.4319924443409474 chr5 180915260 28291908 0.15638209844763787 0.46798899392512133 chr6 171115067 19470723 0.11378730898080412 0.7157101328258051 chr7 159138663 19601679 0.12317358101720384 0.6924636118507528 chr8 146364022 17438263 0.11914309788507998 0.49443961301956746 chr9 141213431 14913274 0.1056080423398253 0.5746843036663495 chr10 135534747 17509922 0.12919138735692626 1.7137106797320287 chr11 135006516 15415697 0.11418483682669064 0.6123376475971051 chr12 133851895 16190569 0.1209588328951189 0.4206835494357278 chr13 115169878 10231821 0.08884112041865669 0.3442464566543882 chr14 107349540 7310965 0.06810429741943934 0.31952587451508846 chr15 102531392 8224323 0.08021273133597952 0.327576960257876 chr16 90354753 10013332 0.11082241572836794 0.7895043993535035 chr17 81195210 9314528 0.11471770317485477 0.5558063300530893 chr18 78077248 7209511 0.0923381802596321 1.0906648121761788 chr19 59128983 6624490 0.11203456687222238 2.3505101557668313 chr20 63025520 6012382 0.09539599197277547 0.37298292023596114 chr21 48129895 4417177 0.0917761611572184 0.40217327105750106 chr22 51304566 3963194 0.07724836810821087 0.3261085567891339 chrMT 16571 637533 38.47281395208497 16.014773491605478 chrX 155270560 14648855 0.09434405981404331 0.4125176966753083 chrY 59373566 912396 0.015367040611978739 0.6138120508458083