BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524875.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 = 1,420,586 number of mapped reads = 1,306,864 (91.99%) number of supplementary alignments = 7,454 (0.52%) number of secondary alignments = 0 number of mapped bases = 76,383,665 bp number of sequenced bases = 76,360,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,420 duplication rate = 1.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9563 >>>>>>> ACTG content number of A's = 20,205,121 bp (26.46%) number of C's = 14,551,938 bp (19.06%) number of T's = 24,133,378 bp (31.6%) number of G's = 17,459,333 bp (22.86%) number of N's = 10,672 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 371,560 number of insertions = 5,258 mapped reads with insertion percentage = 0.4% number of deletions = 14,737 mapped reads with deletion percentage = 1.12% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2569X There is a 2.27% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% 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 6335184 0.025416923635267492 0.499162245105737 chr2 243199373 4963985 0.020411175155455683 0.2508855776636078 chr3 198022430 5501896 0.02778420606190925 0.17599108228476387 chr4 191154276 4192939 0.02193484282820856 0.16584758514486592 chr5 180915260 4590237 0.025372304138412648 0.16909424684618257 chr6 171115067 4982551 0.02911813136829149 0.19808931945480354 chr7 159138663 3511948 0.022068477476149213 0.34960414316798116 chr8 146364022 8301505 0.05671820770270989 0.35030617909631945 chr9 141213431 3133079 0.02218683433872519 0.2097790909633798 chr10 135534747 3771911 0.02782984499170534 0.23835902054651048 chr11 135006516 3648517 0.027024747457374577 0.2331542373914849 chr12 133851895 3015242 0.022526703861757057 0.16164351577396585 chr13 115169878 2020928 0.017547365987485027 0.13945876977778734 chr14 107349540 1628690 0.01517183958124087 0.14196499363979023 chr15 102531392 2242004 0.02186651284320806 0.15771520531214717 chr16 90354753 2148588 0.02377946846913521 0.17895358896201452 chr17 81195210 2046852 0.0252090240298658 0.19019798976406266 chr18 78077248 1853211 0.023735608611615 0.38970979121641103 chr19 59128983 1095056 0.018519784113317152 0.3376880548229427 chr20 63025520 1605718 0.025477266986452474 0.169934399291612 chr21 48129895 1287772 0.026756177215844747 0.18071356219279458 chr22 51304566 450749 0.008785748231453708 0.09852490116537807 chrMT 16571 1603 0.09673526039466537 0.3136249232059502 chrX 155270560 3862577 0.024876428603078395 0.18879827729000367 chrY 59373566 190923 0.0032156229255288454 0.08536902106775213