BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708526.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,189,154 number of mapped reads = 2,068,241 (64.85%) number of supplementary alignments = 602 (0.02%) number of secondary alignments = 0 number of mapped bases = 98,114,711 bp number of sequenced bases = 98,091,342 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,829 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4171 >>>>>>> ACTG content number of A's = 27,608,604 bp (28.15%) number of C's = 18,469,437 bp (18.83%) number of T's = 31,045,968 bp (31.65%) number of G's = 20,966,041 bp (21.37%) number of N's = 1,292 bp (0%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 512,003 number of insertions = 5,495 mapped reads with insertion percentage = 0.26% number of deletions = 15,388 mapped reads with deletion percentage = 0.74% homopolymer indels = 48.47% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.2979X There is a 2.71% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.06% 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% 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 7990807 0.03205932634366435 0.3918770998220099 chr2 243199373 8473522 0.03484187436618103 0.48069564179926744 chr3 198022430 6771175 0.034193979944595165 0.22181296649760615 chr4 191154276 6499443 0.034001033803711514 0.22347705583372204 chr5 180915260 6128254 0.03387361574695247 0.2156158652758034 chr6 171115067 5921902 0.03460771809182648 0.3308197472973035 chr7 159138663 5490980 0.03450437433925155 0.3684092939935345 chr8 146364022 4909424 0.03354256006985105 0.37374146197754393 chr9 141213431 4140873 0.029323506770400614 0.25032090497311316 chr10 135534747 4674212 0.034487185784173854 0.2579925423666113 chr11 135006516 4579495 0.03392054795340397 0.28179624554862903 chr12 133851895 4661078 0.0348226523053708 0.22575903898704938 chr13 115169878 3133475 0.027207417897933347 0.25867538810987734 chr14 107349540 3176079 0.029586330784463537 0.20762500828033512 chr15 102531392 2964393 0.028912052613115795 0.20996596937328643 chr16 90354753 2766064 0.03061337570144207 0.21414033969242838 chr17 81195210 2801198 0.03449954744867339 0.24486205743121667 chr18 78077248 2603200 0.03334133907998397 0.3542192394726586 chr19 59128983 1992170 0.03369193750550386 0.3231163719556201 chr20 63025520 1973469 0.03131222082737278 0.21472321548820364 chr21 48129895 1276785 0.026527899136285255 0.20955345430734756 chr22 51304566 1115704 0.02174668040267605 0.17794218128419198 chrMT 16571 76982 4.6455856616981475 4.889027727110255 chrX 155270560 3294101 0.021215232301603087 0.19500676261988925 chrY 59373566 699926 0.011788512079601215 0.13930346371923125