BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716299.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 = 1,451,960 number of mapped reads = 1,264,434 (87.08%) number of supplementary alignments = 5,784 (0.4%) number of secondary alignments = 0 number of mapped bases = 71,509,917 bp number of sequenced bases = 71,490,702 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,105 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7861 >>>>>>> ACTG content number of A's = 17,927,603 bp (25.08%) number of C's = 13,747,552 bp (19.23%) number of T's = 22,465,023 bp (31.42%) number of G's = 17,349,146 bp (24.27%) number of N's = 1,378 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 361,674 number of insertions = 4,540 mapped reads with insertion percentage = 0.36% number of deletions = 11,237 mapped reads with deletion percentage = 0.88% homopolymer indels = 40.06% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.2011X There is a 2.12% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5805697 0.023292607965056986 0.28102647039182604 chr2 243199373 6007674 0.024702670594467364 0.23128621622644888 chr3 198022430 4761897 0.02404726070677953 0.16621959535692424 chr4 191154276 4556159 0.023834983424592605 0.1793537471571697 chr5 180915260 4312968 0.02383971368694935 0.1666140713298448 chr6 171115067 4030381 0.02355363014292599 0.1719952486444041 chr7 159138663 3883770 0.024404943002443096 0.22272886707177314 chr8 146364022 3570838 0.024396965532964106 0.18857314280482174 chr9 141213431 3006531 0.021290687285970694 0.20534091014467565 chr10 135534747 3412312 0.02517665820411352 0.20918669214756974 chr11 135006516 3289293 0.024363957366324452 0.20205162678128563 chr12 133851895 3212761 0.024002357232222972 0.1678888447205224 chr13 115169878 2217377 0.019253098453399422 0.14755538851590744 chr14 107349540 2157465 0.020097570981673512 0.1575824909844757 chr15 102531392 2085038 0.020335606094180406 0.1527373095343414 chr16 90354753 2177545 0.024099949672819095 0.17844057608582922 chr17 81195210 1997906 0.02460620521826349 0.17430902860229228 chr18 78077248 1915937 0.024538992460389996 0.350880191575028 chr19 59128983 1505353 0.025458800805013 0.23817911468612538 chr20 63025520 1562251 0.024787593977804546 0.17601828117942048 chr21 48129895 939393 0.0195178692993201 0.16565478584051677 chr22 51304566 898942 0.017521676335786565 0.14176920787341882 chrMT 16571 1325 0.0799589644559773 0.2969332490983812 chrX 155270560 3978655 0.02562401397921151 0.19303304607401817 chrY 59373566 222449 0.0037465999599889284 0.09552633783162989