BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068133.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 = 1,754,755
number of mapped reads = 1,253,815 (71.45%)
number of supplementary alignments = 11,301 (0.64%)
number of secondary alignments = 0
number of mapped bases = 82,899,531 bp
number of sequenced bases = 82,865,150 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 129,691
duplication rate = 8.1%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.0134
>>>>>>> ACTG content
number of A's = 22,983,049 bp (27.74%)
number of C's = 14,761,769 bp (17.81%)
number of T's = 26,942,239 bp (32.51%)
number of G's = 18,115,937 bp (21.86%)
number of N's = 62,156 bp (0.08%)
GC percentage = 39.68%
>>>>>>> Mismatches and indels
general error rate = 0.009
number of mismatches = 734,974
number of insertions = 6,509
mapped reads with insertion percentage = 0.51%
number of deletions = 20,726
mapped reads with deletion percentage = 1.64%
homopolymer indels = 47.45%
>>>>>>> Coverage
mean coverageData = 0.0268X
std coverageData = 0.3389X
There is a 1.57% of reference with a coverageData >= 1X
There is a 0.58% of reference with a coverageData >= 2X
There is a 0.25% of reference with a coverageData >= 3X
There is a 0.11% of reference with a coverageData >= 4X
There is a 0.05% of reference with a coverageData >= 5X
There is a 0.03% 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 7459144 0.029926280504633127 0.6301882019590274
chr2 243199373 6914063 0.028429608656926925 0.3212911568776324
chr3 198022430 5629236 0.028427264527558824 0.2694186429428924
chr4 191154276 5545485 0.02901052027734917 0.2710925376873927
chr5 180915260 5102553 0.028204105060015392 0.2667818852452111
chr6 171115067 4430659 0.025892863075581765 0.2756985322328627
chr7 159138663 4295951 0.02699501754642742 0.3562706176636322
chr8 146364022 4024829 0.02749875922376607 0.3633155502599378
chr9 141213431 3642967 0.02579759569753673 0.28910915265214265
chr10 135534747 4406007 0.03250832054159514 0.43332768901716173
chr11 135006516 4250847 0.03148623581990665 0.3149709629672735
chr12 133851895 3757988 0.02807571756828695 0.2672545567091724
chr13 115169878 2495588 0.021668756130834837 0.23843998338752795
chr14 107349540 2332681 0.021729771734466677 0.23466168735584603
chr15 102531392 2064252 0.020132877938495167 0.22125262127338136
chr16 90354753 2179275 0.02411909642429104 0.2586689872687681
chr17 81195210 1855838 0.022856496091333466 0.24504170492342597
chr18 78077248 2242081 0.02871618886977164 0.44740505002599595
chr19 59128983 1362134 0.02303665530658628 0.37937155317007676
chr20 63025520 1598166 0.025357442509002702 0.2663560504225853
chr21 48129895 1122349 0.02331916577004791 0.2545295079747533
chr22 51304566 833310 0.016242413979293772 0.20097518319644522
chrMT 16571 30709 1.853177237342345 2.1755092418005804
chrX 155270560 5043267 0.032480510149509347 0.30367142013660825
chrY 59373566 280152 0.004718463432026299 0.11318200105153838