BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008784.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 = 1,357,152 number of mapped reads = 1,155,183 (85.12%) number of supplementary alignments = 9,327 (0.69%) number of secondary alignments = 0 number of mapped bases = 76,399,543 bp number of sequenced bases = 76,360,737 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 97,232 duplication rate = 6.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4125 >>>>>>> ACTG content number of A's = 20,513,628 bp (26.86%) number of C's = 14,706,448 bp (19.26%) number of T's = 23,643,230 bp (30.96%) number of G's = 17,392,309 bp (22.78%) number of N's = 105,122 bp (0.14%) GC percentage = 42.04% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 677,207 number of insertions = 6,410 mapped reads with insertion percentage = 0.55% number of deletions = 21,276 mapped reads with deletion percentage = 1.82% homopolymer indels = 44.49% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.3352X There is a 1.63% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 9730407 0.03903864696890765 0.485927836126389 chr2 243199373 6100785 0.025085529311788153 0.3822286299171717 chr3 198022430 7527401 0.038012870562188335 0.32660140418884215 chr4 191154276 4245524 0.022209934764943474 0.2444253068212727 chr5 180915260 4249714 0.02349008038349004 0.2161745990483167 chr6 171115067 3268441 0.019100836982403193 0.20404593403932592 chr7 159138663 1830629 0.01150335792377494 0.21341465887107314 chr8 146364022 5550438 0.03792214728835479 0.4243013060942928 chr9 141213431 5187295 0.03673372258761987 0.299242520339035 chr10 135534747 4875436 0.035971853033377486 0.8028020973448812 chr11 135006516 2434505 0.01803250000170362 0.22242888613148545 chr12 133851895 1814029 0.013552508912929473 0.16381059091912503 chr13 115169878 931458 0.008087687650411507 0.12561585142964898 chr14 107349540 3691129 0.034384208819152835 0.27053361225005984 chr15 102531392 837440 0.008167644890649686 0.12541506764036553 chr16 90354753 2709666 0.029989191603456655 0.3345511637337266 chr17 81195210 2861302 0.03523978815991732 0.301286961265839 chr18 78077248 1798171 0.023030665732480735 0.41278989031584645 chr19 59128983 746512 0.012625145269283593 0.275144115165254 chr20 63025520 1659805 0.026335443166514136 0.23755822322337694 chr21 48129895 1678912 0.034882935024063526 0.2887124746410474 chr22 51304566 706300 0.01376680586285439 0.16350482138174374 chrMT 16571 31557 1.9043509745941705 2.1417955574972813 chrX 155270560 1643859 0.010587061706997128 0.1517968136581267 chrY 59373566 288828 0.0048645890664542535 0.179028622985631