BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716754.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 = 2,228,001 number of mapped reads = 1,585,167 (71.15%) number of supplementary alignments = 4,523 (0.2%) number of secondary alignments = 0 number of mapped bases = 85,549,193 bp number of sequenced bases = 85,527,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,056 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.9925 >>>>>>> ACTG content number of A's = 20,254,220 bp (23.68%) number of C's = 17,454,381 bp (20.41%) number of T's = 24,922,832 bp (29.14%) number of G's = 22,893,279 bp (26.77%) number of N's = 2,394 bp (0%) GC percentage = 47.18% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 445,415 number of insertions = 6,239 mapped reads with insertion percentage = 0.39% number of deletions = 13,428 mapped reads with deletion percentage = 0.84% homopolymer indels = 36.03% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.2206X There is a 2.43% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.04% 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% 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 8357305 0.03352972588983038 0.2891656525355712 chr2 243199373 7308139 0.030049991123949155 0.2599220328044306 chr3 198022430 5758211 0.02907857963363039 0.19505711628752226 chr4 191154276 5537407 0.02896826121744721 0.2198886564663323 chr5 180915260 5245266 0.02899294398935723 0.19075458453421826 chr6 171115067 3730545 0.021801382341158772 0.17007292745533562 chr7 159138663 4954475 0.031133069152403273 0.25665307445362046 chr8 146364022 5223284 0.035686939513045086 0.22721204897649186 chr9 141213431 3805504 0.0269485981117476 0.20073962788442315 chr10 135534747 4460375 0.032909457528260265 0.31103001436087707 chr11 135006516 3553377 0.02632004073047852 0.2240611673645348 chr12 133851895 4052694 0.030277449564684908 0.195314785323293 chr13 115169878 1518285 0.013183004326877901 0.1308185274439487 chr14 107349540 2764230 0.02574980759116434 0.18312140911111124 chr15 102531392 1712636 0.016703528222849057 0.15169659000183575 chr16 90354753 2328174 0.025767034081759926 0.19592949618786654 chr17 81195210 3378235 0.04160633367411698 0.24030976934689902 chr18 78077248 2243002 0.028727984879794943 0.23870573605225567 chr19 59128983 2322388 0.03927664374000818 0.2717067972613834 chr20 63025520 2189202 0.034735167595602544 0.21528724133670504 chr21 48129895 1176514 0.024444557795108426 0.19569481255164464 chr22 51304566 950081 0.018518449215611726 0.1544923560949656 chrMT 16571 42759 2.5803512159797237 2.498764466469194 chrX 155270560 2678232 0.017248807500919686 0.16138972591615075 chrY 59373566 258873 0.0043600716184033815 0.13091476422976558