BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524819.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 = 1,674,530 number of mapped reads = 1,506,878 (89.99%) number of supplementary alignments = 5,291 (0.32%) number of secondary alignments = 0 number of mapped bases = 85,264,984 bp number of sequenced bases = 85,237,435 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,821 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1657 >>>>>>> ACTG content number of A's = 20,315,754 bp (23.83%) number of C's = 14,855,812 bp (17.43%) number of T's = 28,301,398 bp (33.2%) number of G's = 21,754,361 bp (25.52%) number of N's = 10,110 bp (0.01%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 438,763 number of insertions = 5,721 mapped reads with insertion percentage = 0.38% number of deletions = 16,906 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2357X There is a 2.48% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6808210 0.02731471629914214 0.27761069286781426 chr2 243199373 7155266 0.029421399865204423 0.37782084085899487 chr3 198022430 5627016 0.028416053676343634 0.18498183370753554 chr4 191154276 5478464 0.02865990818850424 0.2138586560952935 chr5 180915260 5095839 0.028166993762715208 0.1826692992859223 chr6 171115067 4859326 0.028398001912946683 0.2022647545244721 chr7 159138663 4659148 0.029277285055486484 0.28952861666823704 chr8 146364022 4208380 0.02875283107483887 0.20800262880569 chr9 141213431 3635230 0.025742806291563017 0.21174336542454217 chr10 135534747 4143416 0.030570876411493208 0.29055092527486065 chr11 135006516 3834045 0.028398962610071354 0.21776367875908417 chr12 133851895 3869568 0.028909325489937965 0.18741421371804265 chr13 115169878 2630608 0.02284111128432384 0.16537366492636957 chr14 107349540 2576619 0.024002142906248133 0.1750063318619373 chr15 102531392 2465691 0.02404815688057761 0.17511987402407686 chr16 90354753 2618135 0.02897617350578115 0.20419622661389386 chr17 81195210 2454789 0.03023317508508199 0.19677915023094897 chr18 78077248 2215899 0.028380854304700904 0.31388674784607995 chr19 59128983 1850187 0.03129069546147953 0.24577118831803446 chr20 63025520 1841576 0.02921952885117013 0.1975630747375897 chr21 48129895 1119454 0.023259016043978488 0.18415734950389878 chr22 51304566 1086417 0.021175834525137587 0.1604562535990475 chrMT 16571 40404 2.4382354716070243 2.0982543917443235 chrX 155270560 4713839 0.030358871636709497 0.20559489501184777 chrY 59373566 277458 0.004673089704600192 0.13084934387951608