BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525024.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 = 3,830,261
number of mapped reads = 3,509,575 (91.63%)
number of supplementary alignments = 14,524 (0.38%)
number of secondary alignments = 0
number of mapped bases = 205,284,663 bp
number of sequenced bases = 205,217,807 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 252,454
duplication rate = 5.3%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6744
>>>>>>> ACTG content
number of A's = 52,859,994 bp (25.76%)
number of C's = 36,723,268 bp (17.89%)
number of T's = 64,058,491 bp (31.21%)
number of G's = 51,574,029 bp (25.13%)
number of N's = 2,025 bp (0%)
GC percentage = 43.03%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 997,257
number of insertions = 13,437
mapped reads with insertion percentage = 0.38%
number of deletions = 39,842
mapped reads with deletion percentage = 1.13%
homopolymer indels = 43.53%
>>>>>>> Coverage
mean coverageData = 0.0663X
std coverageData = 0.544X
There is a 5.37% of reference with a coverageData >= 1X
There is a 0.87% of reference with a coverageData >= 2X
There is a 0.18% of reference with a coverageData >= 3X
There is a 0.05% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% 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 16470488 0.0660800279410337 1.1058309042284387
chr2 243199373 17387200 0.07149360537208294 0.6145186809872067
chr3 198022430 13474327 0.06804444829810441 0.3176235135966842
chr4 191154276 13275412 0.0694486792437748 0.42132613788122575
chr5 180915260 12230128 0.06760141737076242 0.3157345165156521
chr6 171115067 12199577 0.07129458097339844 0.45326775353397863
chr7 159138663 11323497 0.07115490847123682 0.6352711220935697
chr8 146364022 10467746 0.07151857305479074 0.5983283491429379
chr9 141213431 8455890 0.05988021068619174 0.43552350003213836
chr10 135534747 9803629 0.07233295680258288 0.6041676329450972
chr11 135006516 9390333 0.06955466505038913 0.48005619215416806
chr12 133851895 9277022 0.06930811102823758 0.3278705180698588
chr13 115169878 6435440 0.05587780513234546 0.2846399054472863
chr14 107349540 6130044 0.05710358889288208 0.30626198107038244
chr15 102531392 5758496 0.05616324803236847 0.2971692060345667
chr16 90354753 6074433 0.06722870461501898 0.3493725435137961
chr17 81195210 5613374 0.06913429991744587 0.3833672505439824
chr18 78077248 5524332 0.07075469668193224 0.7901015548062733
chr19 59128983 4196256 0.07096783653458068 0.6631455870497222
chr20 63025520 4407079 0.06992530962061083 0.3315856017333724
chr21 48129895 2713535 0.0563794082659021 0.3655095839675254
chr22 51304566 2489268 0.048519424177567355 0.2612444849222856
chrMT 16571 27088 1.6346629654215195 1.6435329826799847
chrX 155270560 11470035 0.0738712799129468 0.38611638013740535
chrY 59373566 690034 0.011621905950536977 0.3568671033631873