BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716267.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 = 2,321,804 number of mapped reads = 1,656,783 (71.36%) number of supplementary alignments = 1,917 (0.08%) number of secondary alignments = 0 number of mapped bases = 85,800,613 bp number of sequenced bases = 85,781,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 186,808 duplication rate = 9.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.662 >>>>>>> ACTG content number of A's = 18,685,413 bp (21.78%) number of C's = 13,794,807 bp (16.08%) number of T's = 28,360,290 bp (33.06%) number of G's = 24,939,079 bp (29.07%) number of N's = 1,512 bp (0%) GC percentage = 45.15% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 571,042 number of insertions = 5,184 mapped reads with insertion percentage = 0.31% number of deletions = 11,616 mapped reads with deletion percentage = 0.7% homopolymer indels = 40.76% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2442X There is a 2.2% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 7956955 0.03192351123570521 0.2610961973198897 chr2 243199373 6843192 0.028138197543790544 0.40761506756748755 chr3 198022430 5788972 0.029233920622022465 0.21531399494287026 chr4 191154276 5477926 0.028657093707911613 0.21726354703778233 chr5 180915260 5004278 0.027660894940537355 0.20585490655855485 chr6 171115067 3907784 0.022837170732604162 0.2345309097821245 chr7 159138663 4221899 0.02652968750906246 0.22564605757717368 chr8 146364022 5306267 0.036253902615493855 0.24847216164376176 chr9 141213431 4160155 0.029460051855832326 0.23242474137103133 chr10 135534747 4436196 0.03273106047115726 0.2449206751578689 chr11 135006516 3827557 0.028350905670360384 0.23578867814161816 chr12 133851895 4161730 0.031092051405024933 0.22176052641644006 chr13 115169878 1641442 0.014252355116673823 0.15104517274987517 chr14 107349540 3016870 0.028103241057204343 0.21216554809900148 chr15 102531392 1810071 0.01765382254831769 0.16899042108161683 chr16 90354753 2528357 0.02798255671176479 0.22120642430404902 chr17 81195210 3307693 0.04073753858140154 0.2666831553497882 chr18 78077248 2487769 0.031862918631558323 0.2463346142352702 chr19 59128983 2342326 0.03961383878359619 0.3244134680936703 chr20 63025520 2492804 0.03955229564151157 0.26442267200368214 chr21 48129895 1227511 0.02550412794376551 0.20894806727976997 chr22 51304566 1011167 0.019709103474337936 0.18501854677197002 chrMT 16571 6566 0.3962343853720355 0.7545213009121647 chrX 155270560 2621706 0.01688475909406136 0.1695879357164831 chrY 59373566 213420 0.0035945289188121193 0.08861448607940399