BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236119.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 = 1,709,959 number of mapped reads = 1,526,884 (89.29%) number of supplementary alignments = 11,012 (0.64%) number of secondary alignments = 0 number of mapped bases = 104,605,958 bp number of sequenced bases = 104,541,935 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,220 duplication rate = 3.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6889 >>>>>>> ACTG content number of A's = 30,103,422 bp (28.8%) number of C's = 18,930,742 bp (18.11%) number of T's = 33,632,648 bp (32.17%) number of G's = 21,811,844 bp (20.86%) number of N's = 63,279 bp (0.06%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 915,890 number of insertions = 8,810 mapped reads with insertion percentage = 0.57% number of deletions = 36,204 mapped reads with deletion percentage = 2.34% homopolymer indels = 45.88% >>>>>>> Coverage mean coverageData = 0.0338X std coverageData = 0.4496X There is a 2.76% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 9356025 0.037536616608870955 0.6992451149448096 chr2 243199373 6601508 0.027144428534361394 0.3801425034031927 chr3 198022430 4650854 0.023486500998901993 0.17730486754793287 chr4 191154276 4240830 0.022185378683341618 0.22863396028219166 chr5 180915260 5065068 0.027996908607930585 0.19734387542595763 chr6 171115067 10095484 0.05899821784834412 0.3910535823029503 chr7 159138663 7123649 0.04476378565528102 0.4931678643239266 chr8 146364022 7881881 0.05385121898330998 1.2749629976314 chr9 141213431 4975928 0.03523693153521636 0.35059415899139296 chr10 135534747 3762281 0.027758793101225917 0.3358010009981233 chr11 135006516 4670729 0.03459632274341484 0.30894226801248775 chr12 133851895 4347102 0.032476955219797224 0.21392186861074067 chr13 115169878 5492545 0.04769081200207575 0.25668667812862056 chr14 107349540 2829669 0.026359395671374092 0.20128658452719397 chr15 102531392 3586361 0.034978175269482346 0.21760940654609195 chr16 90354753 2027372 0.022437912037676644 0.21312387361177965 chr17 81195210 2733648 0.033667601820353686 0.25378077260239135 chr18 78077248 3262839 0.04178988224584965 0.6735875083996442 chr19 59128983 1668509 0.028218124434847797 0.4333799360278284 chr20 63025520 2021307 0.032071246694989584 0.21671539451460198 chr21 48129895 1835196 0.03813006448486954 0.26196072447649943 chr22 51304566 1003786 0.01956523713698309 0.1598129915700662 chrMT 16571 35988 2.1717458210126126 2.093378467417842 chrX 155270560 5024015 0.03235652012847767 0.23194017607758813 chrY 59373566 313384 0.00527817379202051 0.18050185521917989