BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068140.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 = 2,389,333 number of mapped reads = 2,193,395 (91.8%) number of supplementary alignments = 21,728 (0.91%) number of secondary alignments = 0 number of mapped bases = 147,320,289 bp number of sequenced bases = 147,247,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,323 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4602 >>>>>>> ACTG content number of A's = 41,315,542 bp (28.06%) number of C's = 27,102,577 bp (18.41%) number of T's = 46,805,404 bp (31.79%) number of G's = 32,021,249 bp (21.75%) number of N's = 3,093 bp (0%) GC percentage = 40.15% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,123,316 number of insertions = 11,015 mapped reads with insertion percentage = 0.5% number of deletions = 44,513 mapped reads with deletion percentage = 2.01% homopolymer indels = 46.82% >>>>>>> Coverage mean coverageData = 0.0476X std coverageData = 0.6211X There is a 3.9% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 14097678 0.05656025226111673 1.872464416528951 chr2 243199373 4410793 0.018136531133244326 0.3592902347164212 chr3 198022430 6743640 0.034054930039995976 0.2159922442936614 chr4 191154276 17296562 0.09048482912304823 0.35306563342931946 chr5 180915260 10504430 0.05806270847467483 0.28557226273535585 chr6 171115067 5978393 0.03493785266729317 0.34110836145999623 chr7 159138663 8878873 0.05579331152229173 0.3115319686610093 chr8 146364022 1544587 0.01055305107699213 0.3635887132626964 chr9 141213431 1147007 0.008122506420795058 0.19376106998708872 chr10 135534747 15023159 0.11084359791515308 0.4600132163635668 chr11 135006516 9016810 0.06678796155290756 0.32070645197282127 chr12 133851895 5760017 0.043032763936588274 0.2466191090799994 chr13 115169878 9061189 0.07867672656560425 0.3269965472782624 chr14 107349540 10923424 0.10175566658226948 0.3756375998168634 chr15 102531392 3166010 0.0308784455008667 0.21201696309327253 chr16 90354753 1914660 0.021190473510563412 0.18240184114364474 chr17 81195210 1915005 0.023585196712958806 0.1779933535983311 chr18 78077248 1335590 0.017106007629777115 0.34323394616421704 chr19 59128983 9726235 0.16449183643155169 1.0555966516425361 chr20 63025520 1556889 0.024702517329488118 0.19008281558985504 chr21 48129895 600449 0.01247559339159165 0.12952605138588555 chr22 51304566 401374 0.007823358256261246 0.09998355899665202 chrMT 16571 20785 1.2542996801641422 1.5385239554932093 chrX 155270560 6076091 0.0391322798088704 0.24878558856391453 chrY 59373566 220639 0.0037161150132030136 0.11695080238846733