BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238531.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 = 2,101,226 number of mapped reads = 1,779,268 (84.68%) number of supplementary alignments = 16,628 (0.79%) number of secondary alignments = 0 number of mapped bases = 107,299,737 bp number of sequenced bases = 107,245,358 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 494,365 duplication rate = 19.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.4895 >>>>>>> ACTG content number of A's = 27,057,823 bp (25.23%) number of C's = 18,887,318 bp (17.61%) number of T's = 35,855,855 bp (33.43%) number of G's = 25,437,413 bp (23.72%) number of N's = 6,949 bp (0.01%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 701,336 number of insertions = 6,371 mapped reads with insertion percentage = 0.35% number of deletions = 32,165 mapped reads with deletion percentage = 1.79% homopolymer indels = 40.77% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 0.5979X There is a 1.65% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.13% 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 0.02% 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 0.01% 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 8337672 0.033450957781164366 0.4977977909822001 chr2 243199373 8085922 0.03324812025728372 1.1065156060371746 chr3 198022430 7541059 0.03808184254682664 0.3714776586518143 chr4 191154276 3267714 0.01709464244472355 0.23228647970830013 chr5 180915260 3965944 0.021921555981513113 0.2778095864943403 chr6 171115067 5300980 0.03097903704762597 0.4716318357591204 chr7 159138663 14085628 0.08851166482402834 0.8785630554099179 chr8 146364022 11224356 0.07668794452778839 0.6338887777556524 chr9 141213431 1126831 0.007979630492796397 0.26411044634983866 chr10 135534747 3876046 0.028598171950695417 0.4035628014249409 chr11 135006516 2165439 0.016039514714978647 0.260067224390115 chr12 133851895 1064159 0.007950272201973682 0.17270009123111438 chr13 115169878 1204260 0.010456379922534953 0.31750446008781796 chr14 107349540 577653 0.005381047743660569 0.2847254847435909 chr15 102531392 6191935 0.06039062651173213 0.49318240653677153 chr16 90354753 6254798 0.06922489179954927 0.5488942284015538 chr17 81195210 961068 0.01183651104541758 0.18592684101041299 chr18 78077248 4213427 0.053964850298002305 1.813177998481881 chr19 59128983 1578520 0.026696214274478557 0.5115180994860957 chr20 63025520 1307481 0.020745263188625813 0.4365959163212208 chr21 48129895 7366630 0.15305726305864578 0.7527197374573467 chr22 51304566 208567 0.004065271695310706 0.09304166667599105 chrMT 16571 25911 1.5636352664293043 2.1657302320415726 chrX 155270560 7016194 0.04518689183577363 0.4991895557674454 chrY 59373566 351543 0.005920867208818147 0.20102591996493888