BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716673.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 = 1,967,131
number of mapped reads = 1,844,583 (93.77%)
number of supplementary alignments = 35,810 (1.82%)
number of secondary alignments = 0
number of mapped bases = 145,233,607 bp
number of sequenced bases = 145,166,193 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 77,605
duplication rate = 2.99%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.5885
>>>>>>> ACTG content
number of A's = 37,921,841 bp (26.12%)
number of C's = 28,598,258 bp (19.7%)
number of T's = 44,413,854 bp (30.6%)
number of G's = 34,221,517 bp (23.57%)
number of N's = 10,723 bp (0.01%)
GC percentage = 43.27%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 920,228
number of insertions = 13,614
mapped reads with insertion percentage = 0.73%
number of deletions = 35,263
mapped reads with deletion percentage = 1.88%
homopolymer indels = 40.59%
>>>>>>> Coverage
mean coverageData = 0.0469X
std coverageData = 0.4419X
There is a 3.99% of reference with a coverageData >= 1X
There is a 0.49% 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 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 14199018 0.05696683098735389 0.940292197042822
chr2 243199373 11959523 0.04917579701161483 0.45329106839071903
chr3 198022430 9288262 0.0469051005989574 0.24278959367747638
chr4 191154276 9265449 0.048471052774147726 0.3268720925191361
chr5 180915260 8473148 0.04683489938880778 0.24577669536641208
chr6 171115067 8058952 0.04709668260831759 0.2671751192818496
chr7 159138663 7620532 0.04788611300573765 0.4944724153157931
chr8 146364022 7168706 0.048978607597979236 0.5458362446660128
chr9 141213431 5923763 0.041949005544663805 0.3592433505569518
chr10 135534747 6686312 0.04933282533076186 0.4306784929870635
chr11 135006516 8017046 0.0593826597228833 0.4861682316903772
chr12 133851895 6078117 0.045409271194853086 0.24056570759914772
chr13 115169878 5140774 0.04463644565117973 0.23979800884333557
chr14 107349540 4196692 0.03909371199913852 0.24485176994199664
chr15 102531392 4019880 0.03920633399768921 0.22197648577318968
chr16 90354753 3229344 0.03574072080081941 0.24049265205250134
chr17 81195210 4394557 0.054123352843104905 0.3176844654343129
chr18 78077248 3757526 0.04812574848949594 0.5922069239644531
chr19 59128983 2758659 0.04665493739339302 0.6565491232660153
chr20 63025520 2995435 0.04752733495891823 0.2668379184904597
chr21 48129895 1866807 0.03878684962848974 0.26648177978438214
chr22 51304566 1636229 0.031892463528489845 0.20098813552899436
chrMT 16571 40658 2.4535634542272646 2.012369866800971
chrX 155270560 7996448 0.051500091195652284 0.3071373943083105
chrY 59373566 461770 0.007777366783056285 0.26143463666151595