BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008660.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 = 2,107,875 number of mapped reads = 1,747,941 (82.92%) number of supplementary alignments = 11,657 (0.55%) number of secondary alignments = 0 number of mapped bases = 112,656,445 bp number of sequenced bases = 112,597,746 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 318,869 duplication rate = 12.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1979 >>>>>>> ACTG content number of A's = 29,869,328 bp (26.53%) number of C's = 21,460,806 bp (19.06%) number of T's = 34,882,623 bp (30.98%) number of G's = 26,293,036 bp (23.35%) number of N's = 91,953 bp (0.08%) GC percentage = 42.41% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 995,087 number of insertions = 8,033 mapped reads with insertion percentage = 0.46% number of deletions = 33,516 mapped reads with deletion percentage = 1.9% homopolymer indels = 49.56% >>>>>>> Coverage mean coverageData = 0.0364X std coverageData = 0.4034X There is a 1.65% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.27% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 10097948 0.04051323105830898 0.5054592041226512 chr2 243199373 14864079 0.06111890346033088 0.5550071942965331 chr3 198022430 6307894 0.031854441943773744 0.32456826829125607 chr4 191154276 6865552 0.035916287846995375 0.3596064025992965 chr5 180915260 4215736 0.023302268697510647 0.2794659211181636 chr6 171115067 4400104 0.025714299021955794 0.3178339608183669 chr7 159138663 6362313 0.039979681116209954 0.5305742388871297 chr8 146364022 6780578 0.04632680837371359 0.4352035893270728 chr9 141213431 3989987 0.02825501067246217 0.35012904063829237 chr10 135534747 5784690 0.042680494323717594 0.42408019110601314 chr11 135006516 4772615 0.03535099742889447 0.3972017931720211 chr12 133851895 6677534 0.049887481981484086 0.41596927308298953 chr13 115169878 1861481 0.01616291544565151 0.23298238020339668 chr14 107349540 3910369 0.03642650914014164 0.4043205528438687 chr15 102531392 3818804 0.03724521754274047 0.3905732142844017 chr16 90354753 3896404 0.0431233982787823 0.39279195681576123 chr17 81195210 2280701 0.02808910771953173 0.32541478328282647 chr18 78077248 2418150 0.0309712504211214 0.4705645017244098 chr19 59128983 2162020 0.036564471267838315 0.4041692945952136 chr20 63025520 2295775 0.03642611754730465 0.35651414859623975 chr21 48129895 2111036 0.04386122180403677 0.4006017129226046 chr22 51304566 933065 0.018186782829426918 0.24143485369275888 chrMT 16571 73656 4.444873574316577 4.884802584936994 chrX 155270560 5520544 0.035554351063073385 0.35826205117890386 chrY 59373566 255410 0.00430174599922127 0.1104087262990882