BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716676.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 = 2,326,049 number of mapped reads = 2,099,109 (90.24%) number of supplementary alignments = 11,863 (0.51%) number of secondary alignments = 0 number of mapped bases = 121,113,576 bp number of sequenced bases = 121,081,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,603 duplication rate = 3.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4074 >>>>>>> ACTG content number of A's = 31,031,898 bp (25.63%) number of C's = 22,277,215 bp (18.4%) number of T's = 37,337,773 bp (30.84%) number of G's = 30,433,760 bp (25.13%) number of N's = 784 bp (0%) GC percentage = 43.53% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 593,399 number of insertions = 8,094 mapped reads with insertion percentage = 0.38% number of deletions = 20,425 mapped reads with deletion percentage = 0.97% homopolymer indels = 40.59% >>>>>>> Coverage mean coverageData = 0.0391X std coverageData = 0.3348X There is a 3.37% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% 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 14338229 0.05752534915449619 0.5542130325835359 chr2 243199373 12484576 0.0513347376105283 0.4650917431897581 chr3 198022430 7796897 0.039373807300516414 0.2245935642131738 chr4 191154276 5131166 0.026843061569807626 0.21059029869087595 chr5 180915260 8894347 0.049163055675900416 0.2517109893397115 chr6 171115067 4565722 0.026682174048413866 0.20922918483558473 chr7 159138663 8250162 0.05184259968301983 0.5610417852130523 chr8 146364022 5476465 0.037416743029923025 0.2919400093751279 chr9 141213431 3345682 0.023692378099644078 0.24292756019780046 chr10 135534747 5436976 0.04011499722650458 0.2844773744842985 chr11 135006516 5240998 0.03882033367930182 0.32282187796571704 chr12 133851895 4194620 0.03133777075027589 0.2038752400410023 chr13 115169878 2978914 0.025865391643464273 0.18362039651650422 chr14 107349540 2621747 0.02442252663588498 0.19066195874102737 chr15 102531392 5256530 0.051267518147027596 0.260074839943197 chr16 90354753 3642468 0.04031296505231994 0.24262241308965996 chr17 81195210 4673053 0.05755330887129918 0.29997327228687276 chr18 78077248 3773623 0.04833191610442007 0.5570159588024757 chr19 59128983 1943030 0.03286087298338955 0.4082808916521718 chr20 63025520 3216175 0.051029725736495314 0.2588847208739764 chr21 48129895 1542025 0.03203881911647636 0.2125499030500964 chr22 51304566 1438167 0.028031949437015022 0.18853917187239397 chrMT 16571 3667 0.221290205781184 0.5152300804828918 chrX 155270560 4582986 0.029516129780172106 0.22550526358446726 chrY 59373566 285351 0.0048060276521036316 0.11752744175241689