BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716875.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 = 1,847,614 number of mapped reads = 1,550,853 (83.94%) number of supplementary alignments = 2,744 (0.15%) number of secondary alignments = 0 number of mapped bases = 89,701,864 bp number of sequenced bases = 89,672,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,494 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7716 >>>>>>> ACTG content number of A's = 21,908,607 bp (24.43%) number of C's = 16,610,249 bp (18.52%) number of T's = 28,968,202 bp (32.3%) number of G's = 22,184,831 bp (24.74%) number of N's = 1,021 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 425,778 number of insertions = 6,213 mapped reads with insertion percentage = 0.4% number of deletions = 18,098 mapped reads with deletion percentage = 1.16% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.029X std coverageData = 0.2565X There is a 2.59% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10439861 0.041884994942500066 0.3534405491385761 chr2 243199373 9018188 0.0370814607322199 0.351043172383613 chr3 198022430 5501779 0.02778361521975061 0.18632997259586992 chr4 191154276 3750252 0.01961898043023636 0.16453203367644384 chr5 180915260 7093147 0.039207013272401676 0.21849964967943591 chr6 171115067 3336266 0.01949720768890562 0.17191668568895824 chr7 159138663 6093141 0.03828825054286148 0.45000332234516965 chr8 146364022 3939744 0.026917434668473378 0.2086223797097733 chr9 141213431 2441811 0.017291634249719492 0.19294908650741338 chr10 135534747 4107732 0.030307593373085355 0.3131971612719292 chr11 135006516 3737376 0.02768293050388768 0.23848543001352446 chr12 133851895 3804596 0.028423923322116584 0.18493056751025105 chr13 115169878 2553314 0.022169980938939605 0.16234165017530916 chr14 107349540 1873488 0.01745222196573921 0.14994023748269136 chr15 102531392 3820880 0.03726546500022159 0.21474673337469008 chr16 90354753 2659708 0.029436282117887035 0.20966380920086905 chr17 81195210 3284574 0.04045280503615915 0.2374575488037074 chr18 78077248 2880578 0.036893948926068704 0.39434647139837276 chr19 59128983 1344636 0.02274072598204505 0.27915143922510516 chr20 63025520 2295878 0.03642775180593512 0.210418824030412 chr21 48129895 1112472 0.023113950279758558 0.17407855039510856 chr22 51304566 999567 0.019483002740925633 0.15276055184308623 chrMT 16571 4549 0.274515720234144 0.534138809395397 chrX 155270560 3411883 0.02197379206979095 0.19429491368053092 chrY 59373566 196444 0.003308610434481904 0.08705501259771459