BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716282.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 = 879,800 number of mapped reads = 796,360 (90.52%) number of supplementary alignments = 3,794 (0.43%) number of secondary alignments = 0 number of mapped bases = 45,440,401 bp number of sequenced bases = 45,428,206 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,561 duplication rate = 1.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8433 >>>>>>> ACTG content number of A's = 11,504,748 bp (25.33%) number of C's = 8,702,708 bp (19.16%) number of T's = 14,377,177 bp (31.65%) number of G's = 10,842,594 bp (23.87%) number of N's = 979 bp (0%) GC percentage = 43.02% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 223,432 number of insertions = 3,000 mapped reads with insertion percentage = 0.38% number of deletions = 7,229 mapped reads with deletion percentage = 0.9% homopolymer indels = 41.43% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 0.1474X There is a 1.38% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5505897 0.02208980253654012 0.21507176761149183 chr2 243199373 3704760 0.015233427431574834 0.1600734426196799 chr3 198022430 2932037 0.014806590344336245 0.1282080950177565 chr4 191154276 3070816 0.016064594861587088 0.1381474512223673 chr5 180915260 2207560 0.012202176864461295 0.11589623749551146 chr6 171115067 2351318 0.013741151151815286 0.1260880159343093 chr7 159138663 1937876 0.012177279634427995 0.12873948894726417 chr8 146364022 2810337 0.01920100965796089 0.15653475467208722 chr9 141213431 1661342 0.011764759118415584 0.14944482175168902 chr10 135534747 2157962 0.015921835896443588 0.1768111338021677 chr11 135006516 1427108 0.01057066015983999 0.13057557899137745 chr12 133851895 1993737 0.014895097301386731 0.1287241850192172 chr13 115169878 1350255 0.011724029090314744 0.11233735082779259 chr14 107349540 1558087 0.014514146963275297 0.13070237506926344 chr15 102531392 1377932 0.013439123112656073 0.12085221279641814 chr16 90354753 1289867 0.014275585480267984 0.13169627198494174 chr17 81195210 970415 0.011951628673661906 0.11639587579037793 chr18 78077248 1082642 0.013866293033279041 0.22308643249650284 chr19 59128983 842499 0.014248494684916194 0.15780147788841378 chr20 63025520 1395542 0.022142490851324987 0.1573484648492658 chr21 48129895 583222 0.012117666161540556 0.12573791282776686 chr22 51304566 509922 0.009939115360609424 0.10343830896696199 chrMT 16571 8703 0.5251946171021664 0.7956466863487919 chrX 155270560 2574431 0.016580290558622316 0.14509623953202572 chrY 59373566 136134 0.002292838533565594 0.06929359170175454