BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR8751194.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,174,163
number of mapped reads = 5,130,788 (99.16%)
number of supplementary alignments = 71,907 (1.39%)
number of secondary alignments = 0
number of mapped bases = 507,172,040 bp
number of sequenced bases = 507,048,674 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 61,258
duplication rate = 1.15%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 51.7718
>>>>>>> ACTG content
number of A's = 152,610,959 bp (30.1%)
number of C's = 100,880,815 bp (19.9%)
number of T's = 153,354,997 bp (30.24%)
number of G's = 100,198,112 bp (19.76%)
number of N's = 3,791 bp (0%)
GC percentage = 39.66%
>>>>>>> Mismatches and indels
general error rate = 0.0025
number of mismatches = 1,166,385
number of insertions = 52,902
mapped reads with insertion percentage = 1.02%
number of deletions = 59,999
mapped reads with deletion percentage = 1.16%
homopolymer indels = 48.28%
>>>>>>> Coverage
mean coverageData = 0.1638X
std coverageData = 0.4783X
There is a 12.97% of reference with a coverageData >= 1X
There is a 2.65% of reference with a coverageData >= 2X
There is a 0.57% of reference with a coverageData >= 3X
There is a 0.13% of reference with a coverageData >= 4X
There is a 0.03% 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 69770325 0.27992036577513685 0.6522073035073875
chr2 243199373 38924196 0.16005056065666748 0.46162735770689334
chr3 198022430 35765373 0.18061273664806557 0.48886692904041645
chr4 191154276 26695642 0.1396549559791171 0.42755763150344794
chr5 180915260 41508417 0.22943568718304913 0.5582078618337707
chr6 171115067 29348228 0.17151165303286822 0.48077347660360475
chr7 159138663 29163233 0.18325674258052552 0.4956237341689057
chr8 146364022 26329494 0.179890478822726 0.4994457740965237
chr9 141213431 21475504 0.15207833878067872 0.4554908741562641
chr10 135534747 22578050 0.16658495699261533 0.485674232381829
chr11 135006516 19626026 0.14537095379900034 0.44446661275592203
chr12 133851895 27209767 0.20328264310340918 0.5221657537925871
chr13 115169878 17201129 0.1493544084504457 0.44889756130274855
chr14 107349540 10840851 0.10098646906172118 0.36499592074729764
chr15 102531392 12384321 0.12078565167631783 0.40392011520588533
chr16 90354753 10978875 0.12150854974945258 0.4075017638494819
chr17 81195210 10317171 0.1270662518146083 0.4154045151916715
chr18 78077248 10694260 0.13697024772184593 0.4251239490857956
chr19 59128983 5359121 0.09063441865725984 0.35711880766746773
chr20 63025520 7505886 0.11909280558097736 0.398783611800378
chr21 48129895 6295374 0.13079966203957022 0.42735497319596055
chr22 51304566 3634251 0.07083679452624159 0.31023079513565766
chrMT 16571 242127 14.611489952326354 8.224731263397855
chrX 155270560 22902371 0.14749976428242417 0.44000398779936595
chrY 59373566 422048 0.007108348519945728 0.1026763374258691