BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004046.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,585,237 number of mapped reads = 3,271,219 (91.24%) number of supplementary alignments = 43,012 (1.2%) number of secondary alignments = 0 number of mapped bases = 216,629,073 bp number of sequenced bases = 216,534,497 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 254,067 duplication rate = 5.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7111 >>>>>>> ACTG content number of A's = 60,662,477 bp (28.02%) number of C's = 41,230,444 bp (19.04%) number of T's = 66,809,687 bp (30.85%) number of G's = 47,807,533 bp (22.08%) number of N's = 24,356 bp (0.01%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,667,831 number of insertions = 15,753 mapped reads with insertion percentage = 0.48% number of deletions = 54,292 mapped reads with deletion percentage = 1.64% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.07X std coverageData = 0.657X There is a 4.93% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 23637734 0.09483520604749066 1.2518098873988412 chr2 243199373 12651944 0.05202293017424844 0.6427718950046628 chr3 198022430 10186410 0.051440687804911796 0.3045519310108186 chr4 191154276 15073690 0.07885614863253176 0.4059714576994385 chr5 180915260 15979536 0.08832608150357245 0.40458870921814755 chr6 171115067 13114853 0.0766434728976847 0.44188865155968454 chr7 159138663 13746782 0.08638241481267189 0.9060130662380691 chr8 146364022 11198635 0.07651221145043417 0.9004519352335504 chr9 141213431 9747048 0.06902351944129168 0.6847134777036187 chr10 135534747 7992285 0.05896853151612848 0.5107275991361907 chr11 135006516 6136201 0.045451146965380544 0.45406601799465174 chr12 133851895 9201403 0.06874316572058992 0.36904561780086403 chr13 115169878 8734193 0.07583747722646715 0.36997978342489357 chr14 107349540 7108415 0.0662174705173399 0.42168748225829106 chr15 102531392 5571067 0.054335232276959626 0.3186817142513996 chr16 90354753 5533911 0.06124648473113528 0.422746383381543 chr17 81195210 3936651 0.048483783710886394 0.34606237013705987 chr18 78077248 6903306 0.08841635914216649 1.3905282332987452 chr19 59128983 3069970 0.051919885041824584 0.8632465109387805 chr20 63025520 3032871 0.04812131657144598 0.3293687093180404 chr21 48129895 2861267 0.059448851903790775 0.3811385545708963 chr22 51304566 2550564 0.04971417163922603 0.29340831674265294 chrMT 16571 11399 0.6878884798744795 1.1513468582250184 chrX 155270560 17951238 0.11561263126764018 0.5478665491245303 chrY 59373566 697700 0.01175102064780815 0.2329633813945821