BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867859.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 2,329,614 number of mapped reads = 2,153,338 (92.43%) number of supplementary alignments = 9,991 (0.43%) number of secondary alignments = 0 number of mapped bases = 128,865,716 bp number of sequenced bases = 128,827,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,023 duplication rate = 3.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0757 >>>>>>> ACTG content number of A's = 32,860,874 bp (25.51%) number of C's = 25,535,464 bp (19.82%) number of T's = 39,719,966 bp (30.83%) number of G's = 30,694,641 bp (23.83%) number of N's = 16,659 bp (0.01%) GC percentage = 43.65% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 634,561 number of insertions = 7,596 mapped reads with insertion percentage = 0.35% number of deletions = 23,470 mapped reads with deletion percentage = 1.08% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 0.38X There is a 3.66% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10515134 0.042186992184063604 0.7275950187277319 chr2 243199373 10867390 0.04468510698010722 0.5073419541715815 chr3 198022430 8505347 0.042951432320065965 0.22905932647691263 chr4 191154276 8249559 0.04315654963428597 0.26565455650120096 chr5 180915260 7829404 0.04327663680775187 0.2322777546862225 chr6 171115067 7397442 0.043230804450434514 0.2705982970072669 chr7 159138663 7093140 0.04457207234422976 0.45880586840544435 chr8 146364022 6648685 0.0454256784498584 0.4053744465292484 chr9 141213431 5403320 0.03826349917098183 0.3133983841146343 chr10 135534747 6272225 0.04627761617469209 0.37752944619933887 chr11 135006516 5888784 0.04361851690180643 0.32246568478751314 chr12 133851895 5730509 0.042812311323646185 0.2341837420276085 chr13 115169878 4022990 0.03493092178147484 0.2064633170582257 chr14 107349540 3833299 0.035708574065617796 0.21987410457447323 chr15 102531392 3699662 0.03608321244677923 0.20945825847411778 chr16 90354753 3781034 0.04184654237281795 0.24852005479165362 chr17 81195210 3482436 0.042889672925287094 0.25126172086592785 chr18 78077248 3411754 0.04369716002285327 0.5971612790096394 chr19 59128983 2663359 0.045043206645377275 0.5376737189314421 chr20 63025520 2760772 0.043804033667631775 0.24191169566743057 chr21 48129895 1719989 0.03573639626681089 0.24695255805249794 chr22 51304566 1532153 0.029863872155160613 0.19136628347172233 chrMT 16571 63803 3.8502806107054495 2.896929455587315 chrX 155270560 7081017 0.04560437600018961 0.26252549241281803 chrY 59373566 412509 0.0069476877976303465 0.26776340995731834