BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068952.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 = 1,681,143
number of mapped reads = 1,107,702 (65.89%)
number of supplementary alignments = 4,150 (0.25%)
number of secondary alignments = 0
number of mapped bases = 69,680,182 bp
number of sequenced bases = 69,640,603 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 75,155
duplication rate = 5.84%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.5191
>>>>>>> ACTG content
number of A's = 18,237,591 bp (26.19%)
number of C's = 11,610,804 bp (16.67%)
number of T's = 23,684,569 bp (34.01%)
number of G's = 15,951,146 bp (22.9%)
number of N's = 156,493 bp (0.22%)
GC percentage = 39.58%
>>>>>>> Mismatches and indels
general error rate = 0.0112
number of mismatches = 773,172
number of insertions = 5,967
mapped reads with insertion percentage = 0.53%
number of deletions = 25,439
mapped reads with deletion percentage = 2.27%
homopolymer indels = 49.81%
>>>>>>> Coverage
mean coverageData = 0.0225X
std coverageData = 0.2283X
There is a 1.75% of reference with a coverageData >= 1X
There is a 0.35% of reference with a coverageData >= 2X
There is a 0.09% of reference with a coverageData >= 3X
There is a 0.02% 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 7408654 0.029723713306214792 0.3691690240681378
chr2 243199373 6063774 0.02493334553128145 0.2354616923075776
chr3 198022430 4184950 0.021133717023874517 0.18023614092660312
chr4 191154276 5037070 0.02635080996043217 0.20605779146892844
chr5 180915260 4661605 0.02576678716875514 0.20055973638454616
chr6 171115067 3965951 0.02317709988682645 0.2139055560501417
chr7 159138663 3342812 0.02100565592913144 0.257545910526451
chr8 146364022 4304036 0.02940637966343942 0.2927449259094683
chr9 141213431 2836612 0.0200874093909665 0.21396271474334194
chr10 135534747 3006251 0.02218066633495837 0.2143713323807192
chr11 135006516 3180410 0.023557455552737912 0.2170048503520898
chr12 133851895 3439085 0.025693211142061155 0.2016561639584289
chr13 115169878 1722079 0.014952512149053418 0.1521074971379574
chr14 107349540 1697538 0.01581318373604582 0.16216359958244625
chr15 102531392 1756120 0.01712763248157208 0.16486171383485013
chr16 90354753 1706172 0.01888303540600681 0.17412760899215834
chr17 81195210 1605846 0.019777595254695444 0.18511195887614038
chr18 78077248 1267008 0.01622762113746632 0.2732621220108649
chr19 59128983 990385 0.016749569327109855 0.25397849107406584
chr20 63025520 1425697 0.02262094783192586 0.18845069920575136
chr21 48129895 916043 0.01903272384034912 0.17520463155729857
chr22 51304566 710345 0.013845648747910664 0.14327139281978174
chrMT 16571 85597 5.165469796632672 4.178241267096566
chrX 155270560 4196828 0.027029129024845406 0.2165171408980081
chrY 59373566 169314 0.0028516730829339105 0.07804590118951894