BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240193.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 = 826,821 number of mapped reads = 648,030 (78.38%) number of supplementary alignments = 2,770 (0.34%) number of secondary alignments = 0 number of mapped bases = 41,870,210 bp number of sequenced bases = 41,845,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,258 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8422 >>>>>>> ACTG content number of A's = 12,142,535 bp (29.02%) number of C's = 7,040,674 bp (16.83%) number of T's = 13,178,899 bp (31.49%) number of G's = 9,473,093 bp (22.64%) number of N's = 10,312 bp (0.02%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 468,669 number of insertions = 3,493 mapped reads with insertion percentage = 0.53% number of deletions = 14,390 mapped reads with deletion percentage = 2.19% homopolymer indels = 49.19% >>>>>>> Coverage mean coverageData = 0.0135X std coverageData = 0.1668X There is a 1.22% of reference with a coverageData >= 1X There is a 0.1% 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 3292061 0.013207834695826095 0.23414816956962983 chr2 243199373 4095649 0.01684070542402262 0.18673290486645103 chr3 198022430 2851924 0.014402025063524369 0.13096988724710457 chr4 191154276 2838938 0.014851553726164096 0.13417193318229562 chr5 180915260 2458037 0.013586675883504797 0.1261043599242898 chr6 171115067 2393962 0.013990363572133598 0.13845964417223197 chr7 159138663 2576674 0.016191376447595263 0.24682773468552752 chr8 146364022 2470580 0.016879694656108862 0.28673330362569704 chr9 141213431 1563418 0.011071312331473626 0.1527906065075934 chr10 135534747 1805448 0.01332092352671747 0.14099872439918285 chr11 135006516 1907353 0.014127858836087586 0.15516312500003082 chr12 133851895 1888300 0.014107383388184382 0.12973765282117544 chr13 115169878 1181200 0.01025615395720051 0.10956841145330685 chr14 107349540 1427323 0.013296032754308962 0.129145962766312 chr15 102531392 1062369 0.010361402291309963 0.1132267210121107 chr16 90354753 1074148 0.011888118381553209 0.12170463579277274 chr17 81195210 1034121 0.012736231607751246 0.12832928182141523 chr18 78077248 996236 0.01275961980627186 0.21640489311386257 chr19 59128983 656621 0.0111048925025482 0.15586938197217473 chr20 63025520 815422 0.012937965446377911 0.1259688047742663 chr21 48129895 657819 0.013667576046031266 0.13052523338187466 chr22 51304566 368133 0.0071754432149372434 0.09105841739947317 chrMT 16571 19185 1.1577454589342828 1.4797361424305686 chrX 155270560 2334522 0.01503518761058117 0.13978878805029152 chrY 59373566 100767 0.0016971694103736332 0.050330766049239736