BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716248.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 = 1,848,223 number of mapped reads = 1,755,943 (95.01%) number of supplementary alignments = 37,982 (2.06%) number of secondary alignments = 0 number of mapped bases = 136,576,746 bp number of sequenced bases = 136,525,348 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,706 duplication rate = 3.59% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4868 >>>>>>> ACTG content number of A's = 33,687,246 bp (24.67%) number of C's = 29,621,322 bp (21.7%) number of T's = 39,256,926 bp (28.75%) number of G's = 33,954,859 bp (24.87%) number of N's = 4,995 bp (0%) GC percentage = 46.57% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 871,783 number of insertions = 11,584 mapped reads with insertion percentage = 0.65% number of deletions = 25,197 mapped reads with deletion percentage = 1.41% homopolymer indels = 38.79% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.3509X There is a 3.65% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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 14972394 0.06006963569410726 0.6348054823236694 chr2 243199373 12410323 0.05102942021153977 0.37512135260541085 chr3 198022430 8664204 0.04375364952344035 0.24815000868339376 chr4 191154276 6353969 0.033240004529116574 0.29907036160138983 chr5 180915260 8040318 0.04444245333422952 0.25129726893833076 chr6 171115067 8316647 0.04860265753219733 0.2709986846021577 chr7 159138663 8422319 0.052924404674682984 0.46844698512007027 chr8 146364022 8462783 0.057820104178334206 0.37399293879723217 chr9 141213431 4035603 0.02857803943592306 0.24350479769577402 chr10 135534747 7179888 0.05297451877783046 0.48657888952781325 chr11 135006516 5762321 0.0426817991510869 0.3098542321047841 chr12 133851895 5076865 0.03792897366152343 0.22752750422210613 chr13 115169878 2524136 0.02191663344472762 0.16948971307188349 chr14 107349540 2580332 0.02403673085138511 0.19449692643011343 chr15 102531392 2722276 0.026550658748493338 0.18847886813145226 chr16 90354753 4163437 0.04607878237462505 0.26879209212325156 chr17 81195210 2527215 0.03112517351700919 0.22973546067690204 chr18 78077248 3924944 0.050270009516728865 0.37233412616016565 chr19 59128983 3421734 0.05786898110525594 0.4925295906775477 chr20 63025520 3686192 0.05848729213182216 0.2966893689776689 chr21 48129895 2312109 0.04803893713044668 0.3028532830031256 chr22 51304566 2121629 0.041353609735242665 0.2420778937289521 chrMT 16571 22297 1.3455434192263593 1.424108955929274 chrX 155270560 8438269 0.054345582317729776 0.2858040654034834 chrY 59373566 434542 0.0073187788653287225 0.2676069807738298