BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237860.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,906,027 number of mapped reads = 1,467,387 (76.99%) number of supplementary alignments = 7,022 (0.37%) number of secondary alignments = 0 number of mapped bases = 92,586,604 bp number of sequenced bases = 92,529,645 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 147,342 duplication rate = 8.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3247 >>>>>>> ACTG content number of A's = 24,407,547 bp (26.38%) number of C's = 16,273,038 bp (17.59%) number of T's = 30,056,685 bp (32.48%) number of G's = 21,710,324 bp (23.46%) number of N's = 82,051 bp (0.09%) GC percentage = 41.05% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 824,628 number of insertions = 7,562 mapped reads with insertion percentage = 0.51% number of deletions = 35,138 mapped reads with deletion percentage = 2.36% homopolymer indels = 48.35% >>>>>>> Coverage mean coverageData = 0.0299X std coverageData = 0.2943X There is a 2.03% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 7123129 0.028578179550453355 0.3712097291509803 chr2 243199373 7824240 0.03217212241743732 0.33860076244719023 chr3 198022430 7209177 0.03640586068961986 0.27022644001641694 chr4 191154276 5558244 0.02907726741095763 0.24939978016384176 chr5 180915260 5625307 0.031093601501609096 0.2489961711459616 chr6 171115067 4867970 0.028448517628199273 0.2562048942238854 chr7 159138663 5276217 0.03315484056819052 0.3864670162135537 chr8 146364022 5055603 0.03454129594771589 0.2954900313154621 chr9 141213431 3802138 0.026924761852149884 0.2930932367794533 chr10 135534747 4675725 0.03449834897319726 0.32126900019705257 chr11 135006516 4406727 0.032640846757352064 0.3200625133078053 chr12 133851895 4433513 0.03312252695413838 0.26007640858691516 chr13 115169878 3145154 0.027308824621660188 0.2332845324568981 chr14 107349540 2639071 0.024583905995312138 0.2250834937779973 chr15 102531392 2304860 0.022479554359312707 0.21129518767312752 chr16 90354753 2397296 0.02653204087669854 0.24022394170041958 chr17 81195210 1983375 0.024427241459194452 0.27378194354291197 chr18 78077248 2527846 0.03237621797325643 0.4592659892091809 chr19 59128983 1491064 0.02521714266589026 0.2885123890213575 chr20 63025520 1838376 0.029168755767504974 0.24589993346852163 chr21 48129895 1357734 0.02820978520730203 0.2476069446119614 chr22 51304566 869503 0.016947867758982698 0.17904012585533582 chrMT 16571 65191 3.9340413976223525 3.4638827470727263 chrX 155270560 5837943 0.037598518354026673 0.2854073336173125 chrY 59373566 271201 0.00456770610678833 0.12194697189332986