BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525092.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 = 1,984,239 number of mapped reads = 1,840,182 (92.74%) number of supplementary alignments = 46,562 (2.35%) number of secondary alignments = 0 number of mapped bases = 144,187,456 bp number of sequenced bases = 144,132,471 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,746 duplication rate = 1.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2021 >>>>>>> ACTG content number of A's = 38,275,414 bp (26.56%) number of C's = 29,362,407 bp (20.37%) number of T's = 43,180,613 bp (29.96%) number of G's = 33,308,299 bp (23.11%) number of N's = 5,738 bp (0%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 1,073,589 number of insertions = 12,326 mapped reads with insertion percentage = 0.66% number of deletions = 32,312 mapped reads with deletion percentage = 1.73% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.5066X There is a 4.05% of reference with a coverageData >= 1X There is a 0.4% 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 0.01% 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 14167388 0.056839930601416636 0.9624064370623944 chr2 243199373 11826407 0.04862844362678517 0.6698468369274646 chr3 198022430 9172394 0.04631997496445226 0.23923043501895594 chr4 191154276 8885946 0.04648572967313585 0.2560073234886786 chr5 180915260 8299709 0.045876224039917916 0.24262552247027636 chr6 171115067 8086815 0.04725951455811895 0.2953179381132296 chr7 159138663 7784951 0.04891929373567754 0.7255214996272862 chr8 146364022 7227088 0.04937748977682507 0.6357822792565084 chr9 141213431 5907820 0.041836105518886516 0.44099790054699367 chr10 135534747 6614583 0.048803595730325895 0.5134858278114661 chr11 135006516 8041325 0.059562495487254855 0.5777012940198275 chr12 133851895 6290056 0.04699265557652359 0.2421314765338083 chr13 115169878 5202848 0.04517542338631287 0.2356040271285398 chr14 107349540 4024629 0.03749088258785273 0.2607450376601309 chr15 102531392 3940345 0.03843062035088727 0.21458928678479927 chr16 90354753 3218630 0.03562214375153015 0.24661975271724354 chr17 81195210 4321304 0.05322116908127955 0.32857112820784323 chr18 78077248 3846964 0.04927125505243218 0.83437198626557 chr19 59128983 2755773 0.04660612884209424 0.6848735497054207 chr20 63025520 2780186 0.044112067619592826 0.24181626328733102 chr21 48129895 1900809 0.039493312836024266 0.24481785245376841 chr22 51304566 1514500 0.029519789720080666 0.1875122798436098 chrMT 16571 13405 0.8089433347414158 1.1709716011261522 chrX 155270560 8038910 0.05177356222583341 0.3741308603856653 chrY 59373566 324671 0.005468275225375549 0.13089312725311023