BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717067.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 = 1,057,677 number of mapped reads = 829,241 (78.4%) number of supplementary alignments = 3,166 (0.3%) number of secondary alignments = 0 number of mapped bases = 45,817,078 bp number of sequenced bases = 45,804,087 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,409 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.7963 >>>>>>> ACTG content number of A's = 11,039,720 bp (24.1%) number of C's = 9,557,269 bp (20.87%) number of T's = 13,705,123 bp (29.92%) number of G's = 11,500,662 bp (25.11%) number of N's = 1,313 bp (0%) GC percentage = 45.97% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 248,892 number of insertions = 4,279 mapped reads with insertion percentage = 0.51% number of deletions = 7,911 mapped reads with deletion percentage = 0.94% homopolymer indels = 34.8% >>>>>>> Coverage mean coverageData = 0.0148X std coverageData = 0.1506X There is a 1.36% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4478279 0.017966972286901545 0.17578896381837766 chr2 243199373 3974126 0.01634102074761517 0.1838483083411762 chr3 198022430 3010959 0.015205141154969163 0.13633011419885252 chr4 191154276 2944208 0.015402260737290544 0.1524995510489884 chr5 180915260 2734739 0.01511613227098698 0.13160177180354915 chr6 171115067 1952895 0.011412758877627065 0.11736078142702006 chr7 159138663 2557465 0.01607067039390673 0.16477656452048414 chr8 146364022 2870588 0.019612661368379178 0.15601743489857256 chr9 141213431 2023811 0.014331575868303916 0.13778239219971228 chr10 135534747 2343524 0.017290946062709662 0.23085259871765637 chr11 135006516 1829119 0.013548375694696099 0.14512410870155149 chr12 133851895 2290730 0.01711391534651041 0.14179250119340195 chr13 115169878 841114 0.007303246426986751 0.09212236374864402 chr14 107349540 1536680 0.014314732974170173 0.13139095765255646 chr15 102531392 950346 0.009268829589283252 0.10349797947502554 chr16 90354753 1290216 0.014279448033021572 0.13926106854899364 chr17 81195210 1850126 0.022786147113850682 0.17142853600676722 chr18 78077248 1190512 0.01524787349062303 0.15709498984644582 chr19 59128983 1215950 0.020564365194645745 0.17710282216450585 chr20 63025520 1195408 0.01896704699937422 0.1530707224028929 chr21 48129895 637307 0.013241396018005025 0.13696026738664993 chr22 51304566 529367 0.010318126460713069 0.1102558102395028 chrMT 16571 5976 0.3606300162935248 0.6824999846980964 chrX 155270560 1408804 0.00907322031942179 0.11009955089455443 chrY 59373566 154829 0.00260770929608641 0.09567927960405045