BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6231849.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 = 3,051,677
number of mapped reads = 1,907,580 (62.51%)
number of supplementary alignments = 14,049 (0.46%)
number of secondary alignments = 0
number of mapped bases = 117,821,454 bp
number of sequenced bases = 117,780,116 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 104,900
duplication rate = 2.45%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 41.7673
>>>>>>> ACTG content
number of A's = 33,536,832 bp (28.47%)
number of C's = 24,367,485 bp (20.69%)
number of T's = 31,794,648 bp (26.99%)
number of G's = 28,072,420 bp (23.83%)
number of N's = 8,731 bp (0.01%)
GC percentage = 44.52%
>>>>>>> Mismatches and indels
general error rate = 0.0065
number of mismatches = 755,344
number of insertions = 8,235
mapped reads with insertion percentage = 0.43%
number of deletions = 25,323
mapped reads with deletion percentage = 1.31%
homopolymer indels = 42.33%
>>>>>>> Coverage
mean coverageData = 0.0381X
std coverageData = 5.3563X
There is a 3.3% of reference with a coverageData >= 1X
There is a 0.29% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 8607231 0.03453243552801419 0.8697766113945259
chr2 243199373 8684735 0.03571035111180159 19.058307600234723
chr3 198022430 14565838 0.07355650569483467 0.29838729973610917
chr4 191154276 4876910 0.02551295268958566 0.18666237238064165
chr5 180915260 7863137 0.04346309426855424 0.231441141029043
chr6 171115067 8296223 0.0484832992526602 0.3113076905712609
chr7 159138663 6465280 0.04062670804265837 0.5879728159493234
chr8 146364022 5567003 0.03803532400879227 0.35255469814961243
chr9 141213431 4189965 0.029671150756191172 0.31373365991797325
chr10 135534747 3884772 0.028662553964851536 0.32092396570231374
chr11 135006516 6926126 0.05130216085273988 0.40686850969800775
chr12 133851895 3689079 0.027560902294285785 0.19597537530573259
chr13 115169878 4191320 0.03639250186580904 0.20817390408336223
chr14 107349540 4408163 0.04106364126013023 0.2947496393336489
chr15 102531392 3029246 0.0295445710909689 0.19179887063729303
chr16 90354753 3549883 0.039288281823978866 0.26294450987319856
chr17 81195210 3321139 0.040903139483228136 0.2595213726941719
chr18 78077248 2263266 0.028987522715964577 0.7524675322962621
chr19 59128983 3432811 0.05805631732242038 0.5807349031145324
chr20 63025520 2411168 0.03825701081085884 0.2318830331515704
chr21 48129895 2210149 0.045920503254785826 0.24783977719243902
chr22 51304566 1008499 0.019657100305653107 0.1511946996456806
chrMT 16571 44220 2.668517289240239 2.0818429173263038
chrX 155270560 4062808 0.026165990513591243 0.2363535951614294
chrY 59373566 272483 0.0045892982072190175 0.09587385299454472