BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716870.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 = 1,981,805 number of mapped reads = 1,790,437 (90.34%) number of supplementary alignments = 7,276 (0.37%) number of secondary alignments = 0 number of mapped bases = 102,110,588 bp number of sequenced bases = 102,083,043 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,950 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2102 >>>>>>> ACTG content number of A's = 25,731,044 bp (25.21%) number of C's = 18,890,782 bp (18.51%) number of T's = 31,314,353 bp (30.68%) number of G's = 26,144,641 bp (25.61%) number of N's = 2,223 bp (0%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 493,485 number of insertions = 6,298 mapped reads with insertion percentage = 0.35% number of deletions = 16,339 mapped reads with deletion percentage = 0.91% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.2515X There is a 2.94% of reference with a coverageData >= 1X There is a 0.27% 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 11411469 0.0457831116095795 0.37949782176938135 chr2 243199373 8538938 0.03511085532280546 0.28611469254055694 chr3 198022430 6709084 0.033880424555945504 0.20234485877630393 chr4 191154276 6463528 0.03381314891433556 0.21629539215762386 chr5 180915260 5081038 0.028085181979673798 0.18712072769492494 chr6 171115067 5392107 0.03151158512534726 0.20900697989527475 chr7 159138663 4390691 0.027590347419218925 0.2227256017355641 chr8 146364022 6453802 0.04409418320029495 0.26687627714000606 chr9 141213431 3724961 0.026378234517933353 0.26028542939696386 chr10 135534747 4821492 0.03557384439578435 0.26206682633229095 chr11 135006516 3225439 0.023890987602405798 0.2293460489406236 chr12 133851895 4581823 0.034230542645660715 0.20632768907929247 chr13 115169878 3157497 0.027415996741786946 0.17964547856148538 chr14 107349540 3584772 0.033393454690164484 0.2129958765708528 chr15 102531392 2950374 0.028775323756454998 0.18705711391760427 chr16 90354753 3050297 0.033759120563364275 0.22003426507391427 chr17 81195210 2328299 0.028675324566560023 0.1927565761803304 chr18 78077248 2512498 0.03217964342185831 0.46981350339785494 chr19 59128983 1950441 0.03298620914890418 0.2929202317643033 chr20 63025520 3183418 0.05050998389223921 0.2544512022221945 chr21 48129895 1324572 0.02752077477002599 0.20139155099318712 chr22 51304566 1234336 0.02405898921355265 0.1696079107079452 chrMT 16571 5445 0.3285860841228653 0.6394513279694495 chrX 155270560 5742119 0.036981376250591225 0.23934656306301164 chrY 59373566 292148 0.004920506206415158 0.109824958758856