BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524367.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 = 2,036,254 number of mapped reads = 1,880,425 (92.35%) number of supplementary alignments = 8,476 (0.42%) number of secondary alignments = 0 number of mapped bases = 109,853,425 bp number of sequenced bases = 109,819,984 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 84,859 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7319 >>>>>>> ACTG content number of A's = 28,597,873 bp (26.04%) number of C's = 20,618,852 bp (18.78%) number of T's = 33,511,673 bp (30.52%) number of G's = 27,089,514 bp (24.67%) number of N's = 2,072 bp (0%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 549,064 number of insertions = 9,024 mapped reads with insertion percentage = 0.48% number of deletions = 20,664 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.13% >>>>>>> Coverage mean coverageData = 0.0355X std coverageData = 0.3176X There is a 3.13% of reference with a coverageData >= 1X There is a 0.3% 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 9225560 0.03701318762210827 0.48559066546306556 chr2 243199373 8620211 0.03544503792779104 0.4823435333386239 chr3 198022430 6263798 0.031631760099095844 0.19722483206603192 chr4 191154276 6796531 0.035555213005018 0.26494078535492527 chr5 180915260 6221625 0.0343897192530912 0.20458212426119024 chr6 171115067 5818811 0.034005252150005 0.23712588766517056 chr7 159138663 6219400 0.039081640393070285 0.3953189716942463 chr8 146364022 5839224 0.039895214139442 0.4202066543735935 chr9 141213431 3652269 0.025863467618742298 0.2279354190911881 chr10 135534747 4894906 0.036115506232508775 0.3426682478615526 chr11 135006516 3956699 0.0293074669077454 0.24842288110514055 chr12 133851895 5440128 0.04064289115966569 0.225572150492302 chr13 115169878 3293505 0.028596930527268596 0.18760845158012956 chr14 107349540 3722436 0.0346758449081384 0.2120698116901891 chr15 102531392 3927759 0.038307867701630346 0.2209139013831368 chr16 90354753 3761326 0.041628424350847376 0.24023457312316046 chr17 81195210 4847038 0.05969610768911122 0.2874737834110261 chr18 78077248 2071203 0.026527612756023368 0.3875771194999014 chr19 59128983 2860813 0.048382584222698366 0.38766305365254144 chr20 63025520 3680687 0.05839994656132944 0.28469638521972074 chr21 48129895 1417442 0.029450344738961097 0.24425464146261158 chr22 51304566 1033354 0.02014156010987404 0.15589390099596212 chrMT 16571 53896 3.2524289421278136 2.613018873986055 chrX 155270560 5829949 0.03754703402885905 0.23106886019484896 chrY 59373566 404855 0.00681877521050361 0.29273991530381627