BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716757.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 = 465,375 number of mapped reads = 419,157 (90.07%) number of supplementary alignments = 2,196 (0.47%) number of secondary alignments = 0 number of mapped bases = 24,290,421 bp number of sequenced bases = 24,283,094 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,523 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3265 >>>>>>> ACTG content number of A's = 6,241,406 bp (25.7%) number of C's = 4,550,348 bp (18.74%) number of T's = 7,797,807 bp (32.11%) number of G's = 5,692,849 bp (23.44%) number of N's = 684 bp (0%) GC percentage = 42.18% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 124,137 number of insertions = 1,642 mapped reads with insertion percentage = 0.39% number of deletions = 4,620 mapped reads with deletion percentage = 1.1% homopolymer indels = 41.01% >>>>>>> Coverage mean coverageData = 0.0078X std coverageData = 0.1057X There is a 0.75% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1930568 0.007745489227888423 0.15487539181911028 chr2 243199373 2043602 0.00840299041395966 0.12234864148122475 chr3 198022430 1621978 0.008190880194733496 0.09327168833878666 chr4 191154276 1556838 0.008144405830607734 0.09521869245982974 chr5 180915260 1479177 0.008176076468065768 0.09308666019074528 chr6 171115067 1384173 0.00808913571590981 0.09771923900304769 chr7 159138663 1328417 0.008347544053452303 0.11686213246044727 chr8 146364022 1231014 0.008410632498196858 0.10339367714986764 chr9 141213431 980312 0.006942059215316424 0.09277109617435636 chr10 135534747 1178624 0.008696102114685026 0.1085962047434688 chr11 135006516 1081881 0.008013546546153372 0.09935511518032837 chr12 133851895 1085207 0.008107520629424035 0.09308024903937218 chr13 115169878 861846 0.0074832587736178725 0.08950811291984478 chr14 107349540 732889 0.006827127531240469 0.08647194824692724 chr15 102531392 696692 0.006794914088360373 0.08513293092600886 chr16 90354753 692802 0.007667576712870877 0.09253494862078442 chr17 81195210 625990 0.0077096912490281135 0.09182474751441325 chr18 78077248 629632 0.008064218656887088 0.1355334374522939 chr19 59128983 487783 0.0082494738663102 0.11960547358386485 chr20 63025520 520399 0.008256956864457446 0.09458573583214205 chr21 48129895 341738 0.0071003271459453635 0.08975244515390471 chr22 51304566 280914 0.005475419088429673 0.07607159629184289 chrMT 16571 13269 0.8007362259368777 0.9813919851897854 chrX 155270560 1426458 0.009186918627716678 0.10241664506067188 chrY 59373566 78218 0.001317387606464466 0.04911639998069963