BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751199.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 = 7,335,726 number of mapped reads = 7,269,128 (99.09%) number of supplementary alignments = 195,389 (2.66%) number of secondary alignments = 0 number of mapped bases = 1,050,029,090 bp number of sequenced bases = 1,049,715,153 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,161,673 duplication rate = 15.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.7643 >>>>>>> ACTG content number of A's = 297,203,034 bp (28.31%) number of C's = 228,184,960 bp (21.74%) number of T's = 299,730,483 bp (28.55%) number of G's = 224,586,604 bp (21.4%) number of N's = 10,072 bp (0%) GC percentage = 43.13% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 7,333,170 number of insertions = 210,582 mapped reads with insertion percentage = 2.81% number of deletions = 123,677 mapped reads with deletion percentage = 1.66% homopolymer indels = 49.29% >>>>>>> Coverage mean coverageData = 0.3392X std coverageData = 1.3051X There is a 19.38% of reference with a coverageData >= 1X There is a 7.77% of reference with a coverageData >= 2X There is a 3.31% of reference with a coverageData >= 3X There is a 1.51% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.38% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 113450526 0.45516647278483613 2.8023840387986354 chr2 243199373 83032740 0.34141839666667234 1.029466807419366 chr3 198022430 70601129 0.356530969749235 0.9103636644879756 chr4 191154276 48662305 0.2545708420354667 0.7972589826903952 chr5 180915260 88490669 0.48912772200642446 1.0917437219119825 chr6 171115067 59631917 0.34849015954860363 1.1287227550208847 chr7 159138663 60527606 0.38034507051250016 1.1359262201082223 chr8 146364022 53253386 0.36384205129317915 0.9759357318647063 chr9 141213431 47628500 0.3372802407159132 1.1045345512208704 chr10 135534747 50870473 0.37533159670117655 1.9184582925832954 chr11 135006516 46905654 0.347432519479282 1.146736714827282 chr12 133851895 56501258 0.42211772945015086 0.989378223871888 chr13 115169878 23568756 0.2046434051097979 0.6652857876164985 chr14 107349540 25242935 0.23514711846925473 0.8906280023303341 chr15 102531392 26343249 0.25692861948075374 0.7729509830018122 chr16 90354753 31187967 0.34517240061516186 0.9522686844576623 chr17 81195210 33647806 0.4144062931791173 1.1820873198675201 chr18 78077248 21260678 0.2723031170360923 1.2722699613314072 chr19 59128983 16327089 0.27612666701877825 1.9146187926958222 chr20 63025520 20696429 0.32838172537092913 0.8869114820167464 chr21 48129895 14375389 0.29867900189684604 0.8778320111920004 chr22 51304566 12916249 0.2517563251582715 0.772621985918978 chrMT 16571 561143 33.86295335224187 14.829410508098865 chrX 155270560 43323704 0.2790207235679449 0.8230489952145204 chrY 59373566 1021533 0.017205181848097183 0.42130150345828626