BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524624.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 = 1,850,388 number of mapped reads = 1,722,017 (93.06%) number of supplementary alignments = 3,924 (0.21%) number of secondary alignments = 0 number of mapped bases = 100,357,261 bp number of sequenced bases = 100,324,693 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,072 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2908 >>>>>>> ACTG content number of A's = 24,065,229 bp (23.99%) number of C's = 19,289,024 bp (19.23%) number of T's = 33,243,091 bp (33.14%) number of G's = 23,726,744 bp (23.65%) number of N's = 605 bp (0%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 470,861 number of insertions = 7,011 mapped reads with insertion percentage = 0.41% number of deletions = 19,185 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.27% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.2827X There is a 2.84% of reference with a coverageData >= 1X There is a 0.29% 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 10248324 0.04111654349699694 0.4867292566883533 chr2 243199373 8828624 0.03630200148583442 0.32224427846185677 chr3 198022430 6294052 0.031784540771467154 0.19838867192370624 chr4 191154276 4541915 0.023760467696783305 0.19759001974006435 chr5 180915260 6031291 0.033337657641483644 0.20431922834270336 chr6 171115067 6992205 0.04086259101894282 0.23945563287143792 chr7 159138663 6044770 0.03798429549455245 0.38607192107048044 chr8 146364022 8820952 0.0602672151220332 0.3808476283612699 chr9 141213431 3572304 0.025297197120010488 0.24929757991142368 chr10 135534747 4244929 0.03131985777787301 0.278074219856283 chr11 135006516 5085007 0.03766490055931819 0.27560608213035886 chr12 133851895 3302271 0.024671081421746028 0.18018373852030095 chr13 115169878 2972976 0.025813833023249362 0.17952185172920995 chr14 107349540 1859457 0.017321518098726833 0.15413752743966336 chr15 102531392 2474375 0.0241328528925073 0.18557719998498198 chr16 90354753 2921103 0.032329267725406764 0.21201441773384763 chr17 81195210 2164996 0.02666408523359937 0.19115580997135437 chr18 78077248 2671294 0.03421347535200011 0.40815965200827503 chr19 59128983 1934009 0.032708308208176017 0.3439718550898587 chr20 63025520 1850093 0.029354664586662672 0.19481667847306444 chr21 48129895 878703 0.01825690664814457 0.16972026109460503 chr22 51304566 1763624 0.03437557585030541 0.20728305146951226 chrMT 16571 51493 3.1074165711182187 2.463205686538296 chrX 155270560 4558327 0.02935731667355357 0.21892528177327772 chrY 59373566 250167 0.004213440708614335 0.12077850785091347