BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525118.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 = 1,126,609 number of mapped reads = 1,031,786 (91.58%) number of supplementary alignments = 27,638 (2.45%) number of secondary alignments = 0 number of mapped bases = 78,174,916 bp number of sequenced bases = 78,145,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,436 duplication rate = 1.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8343 >>>>>>> ACTG content number of A's = 21,218,404 bp (27.15%) number of C's = 15,933,303 bp (20.39%) number of T's = 23,407,327 bp (29.95%) number of G's = 17,583,277 bp (22.5%) number of N's = 2,828 bp (0%) GC percentage = 42.89% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 556,029 number of insertions = 7,126 mapped reads with insertion percentage = 0.68% number of deletions = 17,408 mapped reads with deletion percentage = 1.67% homopolymer indels = 41.39% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.2837X There is a 2.28% of reference with a coverageData >= 1X There is a 0.17% 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 7773441 0.03118724827570239 0.4739242249530789 chr2 243199373 6701713 0.027556456734779494 0.38270545660009164 chr3 198022430 5199153 0.026255374201801282 0.17349141885585087 chr4 191154276 4825731 0.02524521606830286 0.17548686288379226 chr5 180915260 4757984 0.026299517243597914 0.17721328935513062 chr6 171115067 4513229 0.026375403867854606 0.19319299888975341 chr7 159138663 4334612 0.027237956624029197 0.4088296066980607 chr8 146364022 2200479 0.015034288959345487 0.3433668790039987 chr9 141213431 3261027 0.02309289546261361 0.25852045283430203 chr10 135534747 3617506 0.026690616834958197 0.27323775203538864 chr11 135006516 4394104 0.03254734756654264 0.35032733518882625 chr12 133851895 3504152 0.026179323049554136 0.17518274108713877 chr13 115169878 2838662 0.02464760794484822 0.16893308032322302 chr14 107349540 2361985 0.0220027491501128 0.1768446628053143 chr15 102531392 2220672 0.02165845948916796 0.1573551434079574 chr16 90354753 1727670 0.019120964228633328 0.16060939671240443 chr17 81195210 2341127 0.028833314181957285 0.21239618471861976 chr18 78077248 2060666 0.02639265666740713 0.4193730970012338 chr19 59128983 1500873 0.025383034238894316 0.3598231975616693 chr20 63025520 1557072 0.02470542091521022 0.16987789165042536 chr21 48129895 1020182 0.021196431033144784 0.16512045221275776 chr22 51304566 806973 0.015729067857235164 0.13373025238980032 chrMT 16571 3298 0.19902238851004767 0.5187348893516077 chrX 155270560 4475112 0.02882138120710069 0.23539320894403507 chrY 59373566 177493 0.002989427988879765 0.07242945526696196