BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716743.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 = 589,755
number of mapped reads = 447,106 (75.81%)
number of supplementary alignments = 749 (0.13%)
number of secondary alignments = 0
number of mapped bases = 23,662,402 bp
number of sequenced bases = 23,656,496 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 23,742
duplication rate = 4.76%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.0879
>>>>>>> ACTG content
number of A's = 5,122,165 bp (21.65%)
number of C's = 3,936,607 bp (16.64%)
number of T's = 7,663,445 bp (32.39%)
number of G's = 6,933,907 bp (29.31%)
number of N's = 372 bp (0%)
GC percentage = 45.95%
>>>>>>> Mismatches and indels
general error rate = 0.0067
number of mismatches = 156,657
number of insertions = 1,325
mapped reads with insertion percentage = 0.3%
number of deletions = 3,411
mapped reads with deletion percentage = 0.76%
homopolymer indels = 38.79%
>>>>>>> Coverage
mean coverageData = 0.0076X
std coverageData = 0.102X
There is a 0.7% of reference with a coverageData >= 1X
There is a 0.05% 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 2307731 0.009258677032543882 0.11531355590375383
chr2 243199373 2077306 0.008541576297567181 0.13761867449928655
chr3 198022430 1624311 0.008202661688375404 0.09849494647060224
chr4 191154276 1502325 0.00785922779985314 0.0978102377995529
chr5 180915260 1457854 0.008058214658066987 0.09738024254455577
chr6 171115067 1035189 0.0060496659829493565 0.09167047884581106
chr7 159138663 1377327 0.008654886085099256 0.10889410999223244
chr8 146364022 1474470 0.010073992090761211 0.1115387986406696
chr9 141213431 1044903 0.007399459050038944 0.09629873761396938
chr10 135534747 1198634 0.008843739531974041 0.10732284084610436
chr11 135006516 1027560 0.007611188188872306 0.09898992403164869
chr12 133851895 1114452 0.008326008384117387 0.0996190628842139
chr13 115169878 413220 0.003587917319839481 0.06577583643047881
chr14 107349540 730726 0.0068069783997211355 0.0902412135186516
chr15 102531392 463671 0.004522234517210105 0.07273360110214548
chr16 90354753 616614 0.006824367059030088 0.09195178828229175
chr17 81195210 927276 0.011420328859300936 0.1211196092144304
chr18 78077248 645361 0.008265672990933287 0.10667577533247122
chr19 59128983 624291 0.010558121725178327 0.12298117395058043
chr20 63025520 606444 0.00962219748444757 0.10831144223452754
chr21 48129895 321830 0.006686696490819271 0.0916010340802939
chr22 51304566 263831 0.005142446775594983 0.0794742702621661
chrMT 16571 16463 0.9934825900669845 1.2383375719289982
chrX 155270560 723510 0.004659672767329493 0.07479819506927417
chrY 59373566 67103 0.0011301830851796909 0.041573211529265804