BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716553.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 = 2,128,373 number of mapped reads = 1,812,292 (85.15%) number of supplementary alignments = 7,547 (0.35%) number of secondary alignments = 0 number of mapped bases = 102,459,456 bp number of sequenced bases = 102,429,559 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,155 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.223 >>>>>>> ACTG content number of A's = 25,993,897 bp (25.38%) number of C's = 19,953,840 bp (19.48%) number of T's = 32,158,385 bp (31.4%) number of G's = 24,322,636 bp (23.75%) number of N's = 801 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 542,131 number of insertions = 6,596 mapped reads with insertion percentage = 0.36% number of deletions = 18,749 mapped reads with deletion percentage = 1.03% homopolymer indels = 39.6% >>>>>>> Coverage mean coverageData = 0.0331X std coverageData = 0.2705X There is a 2.96% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8739870 0.03506458665954537 0.35156570055941794 chr2 243199373 8006711 0.03292241629257819 0.40260510867925997 chr3 198022430 5927331 0.029932624299176612 0.19574666529161483 chr4 191154276 6274390 0.032823696813353 0.21697801449244808 chr5 180915260 5802545 0.0320732756319174 0.1952635224013292 chr6 171115067 5493585 0.03210462466171959 0.23444005678850782 chr7 159138663 5891993 0.0370242710911804 0.3937503976374263 chr8 146364022 5281703 0.03608607448625592 0.264242366910267 chr9 141213431 3452460 0.024448524305028748 0.2029588986252997 chr10 135534747 4619105 0.03408059632117807 0.33504057025055933 chr11 135006516 3671457 0.02719466518193833 0.22169812243300713 chr12 133851895 5132255 0.03834278924478432 0.2172587193513477 chr13 115169878 3064213 0.026606028010205934 0.17810877511928289 chr14 107349540 3389004 0.03156980458416496 0.20315574607067266 chr15 102531392 3705104 0.03613628887433812 0.2138894076248882 chr16 90354753 3473264 0.03844030208349969 0.23028630432019462 chr17 81195210 4561560 0.0561801613666619 0.27635764946410635 chr18 78077248 1915319 0.024531077222393904 0.3142812861029868 chr19 59128983 2762375 0.046717783054039674 0.33564576413140085 chr20 63025520 3313287 0.05257056189302365 0.2664803561817334 chr21 48129895 1279560 0.026585555609460607 0.19348897485295719 chr22 51304566 940186 0.018325581391722523 0.14794205297783947 chrMT 16571 2511 0.15152978094261058 0.5332361794753822 chrX 155270560 5453696 0.035123825147536016 0.2207391429580553 chrY 59373566 305972 0.005153337092806587 0.14316802748607144