BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524963.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 = 2,417,198 number of mapped reads = 2,240,822 (92.7%) number of supplementary alignments = 5,611 (0.23%) number of secondary alignments = 0 number of mapped bases = 131,143,011 bp number of sequenced bases = 131,099,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,705 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6238 >>>>>>> ACTG content number of A's = 32,916,983 bp (25.11%) number of C's = 23,237,867 bp (17.73%) number of T's = 42,845,365 bp (32.68%) number of G's = 32,098,078 bp (24.48%) number of N's = 1,392 bp (0%) GC percentage = 42.21% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 642,284 number of insertions = 8,889 mapped reads with insertion percentage = 0.39% number of deletions = 25,455 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.0424X std coverageData = 0.3826X There is a 3.72% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14427463 0.05788335829261585 0.796239603226259 chr2 243199373 10101708 0.04153673537636958 0.4144248772207368 chr3 198022430 7554031 0.038147350277440796 0.2197898820519044 chr4 191154276 9004762 0.047107300911228375 0.2608886070951774 chr5 180915260 5948191 0.032878326571235614 0.20590914273921063 chr6 171115067 7965057 0.04654795828119566 0.379391429390244 chr7 159138663 8034045 0.05048455760873145 0.5274438606702143 chr8 146364022 8191520 0.05596675937205388 0.36899426143015507 chr9 141213431 3770926 0.02670373471769835 0.2821062566790332 chr10 135534747 6943277 0.05122875981020572 0.3754196654834252 chr11 135006516 5692444 0.04216421672565789 0.3314406142775347 chr12 133851895 7214697 0.0539005966258453 0.2601130640155138 chr13 115169878 2691789 0.023372335255925164 0.17029808741353497 chr14 107349540 3124299 0.02910398125599793 0.1984719872998269 chr15 102531392 3728847 0.036367856977890245 0.2280971948036838 chr16 90354753 4285154 0.04742588361677 0.2586124724599719 chr17 81195210 3262688 0.040183257115783064 0.3252300720412988 chr18 78077248 2738267 0.035071254048298424 0.48148239333274584 chr19 59128983 3223122 0.05451001922356757 0.43787415813869235 chr20 63025520 3224228 0.051157499374856405 0.254503413110049 chr21 48129895 1982035 0.04118095416580485 0.23881147344165626 chr22 51304566 1752907 0.03416668606065199 0.20313595376938073 chrMT 16571 160728 9.699354293645525 6.414630512924568 chrX 155270560 5770362 0.03716327164660191 0.25913126872975256 chrY 59373566 350464 0.005902694138330853 0.1315454019693774