BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716666.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 = 2,413,843 number of mapped reads = 2,242,224 (92.89%) number of supplementary alignments = 42,958 (1.78%) number of secondary alignments = 0 number of mapped bases = 177,960,490 bp number of sequenced bases = 177,878,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 106,218 duplication rate = 3.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4883 >>>>>>> ACTG content number of A's = 46,543,688 bp (26.17%) number of C's = 33,592,174 bp (18.88%) number of T's = 53,909,067 bp (30.31%) number of G's = 43,820,440 bp (24.64%) number of N's = 12,957 bp (0.01%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,145,741 number of insertions = 15,136 mapped reads with insertion percentage = 0.66% number of deletions = 42,904 mapped reads with deletion percentage = 1.88% homopolymer indels = 42.76% >>>>>>> Coverage mean coverageData = 0.0575X std coverageData = 0.5123X There is a 4.75% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 17287500 0.06935790141923057 1.0675229756033355 chr2 243199373 14462453 0.05946747650537734 0.5729096474698182 chr3 198022430 11402906 0.057583911075124165 0.2761577372438344 chr4 191154276 11459960 0.0599513661938695 0.3824408821982405 chr5 180915260 10246811 0.05663873240985862 0.27712290166925685 chr6 171115067 9815112 0.057359718066206294 0.3018186528973846 chr7 159138663 9311277 0.058510463921642976 0.6136062619063011 chr8 146364022 8785492 0.06002494246844351 0.5898750669056271 chr9 141213431 7156610 0.05067938615555627 0.4317695167523794 chr10 135534747 8230277 0.06072447975278251 0.5035008248583961 chr11 135006516 9770328 0.07236930697478335 0.5679964747623293 chr12 133851895 7773222 0.0580733055740451 0.28022603757470455 chr13 115169878 5962727 0.05177332045102974 0.2653618948623395 chr14 107349540 5138874 0.047870479929397 0.2780386283560545 chr15 102531392 5015295 0.04891472652590145 0.25436092050176895 chr16 90354753 4070524 0.04505046901074479 0.2789223101836066 chr17 81195210 5637898 0.06943633743911741 0.37827313354705355 chr18 78077248 4590421 0.05879332478521784 0.7323248135954477 chr19 59128983 3377111 0.057114308899918 0.6931526496090762 chr20 63025520 3642230 0.05778976516179478 0.29993852484173467 chr21 48129895 2311498 0.04802624231779438 0.3135256064618066 chr22 51304566 2063057 0.04021195696305081 0.23441677379309592 chrMT 16571 54273 3.2751795305050995 2.5360491208709406 chrX 155270560 9838093 0.06336096810625272 0.3508709686670459 chrY 59373566 556541 0.009373548491259561 0.3089817121045003