BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472842.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,393,458
number of mapped reads = 2,125,334 (88.8%)
number of supplementary alignments = 12,377 (0.52%)
number of secondary alignments = 0
number of mapped bases = 138,799,280 bp
number of sequenced bases = 138,743,629 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 72,559
duplication rate = 2.69%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9522
>>>>>>> ACTG content
number of A's = 36,834,448 bp (26.55%)
number of C's = 27,350,746 bp (19.71%)
number of T's = 41,825,029 bp (30.15%)
number of G's = 32,730,499 bp (23.59%)
number of N's = 2,907 bp (0%)
GC percentage = 43.3%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 1,166,392
number of insertions = 10,501
mapped reads with insertion percentage = 0.49%
number of deletions = 31,324
mapped reads with deletion percentage = 1.46%
homopolymer indels = 45.81%
>>>>>>> Coverage
mean coverageData = 0.0448X
std coverageData = 0.323X
There is a 3.87% of reference with a coverageData >= 1X
There is a 0.46% of reference with a coverageData >= 2X
There is a 0.07% 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 10225105 0.04102338826269163 0.40976904282350973
chr2 243199373 13613316 0.05597595023404933 0.45216233909878384
chr3 198022430 10210722 0.051563461775517044 0.25417316053490935
chr4 191154276 7659091 0.04006758917598056 0.24325910468345044
chr5 180915260 6140588 0.03394179131157869 0.20724815607020547
chr6 171115067 8496227 0.04965212677618856 0.2687628632346741
chr7 159138663 8455462 0.05313266958891065 0.4357720478070313
chr8 146364022 7889568 0.05390373872070829 0.33385611429044065
chr9 141213431 7998083 0.056638259855041694 0.3733119103397676
chr10 135534747 5753364 0.04244936540147893 0.2995545609813383
chr11 135006516 4671959 0.03460543341478422 0.31467397944981657
chr12 133851895 6038318 0.045111935098117215 0.2446572219512911
chr13 115169878 5493353 0.04769782772540577 0.2517813913914948
chr14 107349540 3209477 0.029897445298787493 0.2185937577345691
chr15 102531392 2690922 0.02624485972062098 0.18833944638324251
chr16 90354753 4710785 0.05213654892067493 0.2778268638996955
chr17 81195210 3134725 0.03860726513300477 0.23768048933626965
chr18 78077248 2356849 0.030186117727919917 0.581988441261997
chr19 59128983 3198015 0.05408540512188414 0.3463827627520788
chr20 63025520 6039857 0.09583192649580678 0.3676102447612989
chr21 48129895 1763805 0.03664676600686538 0.25235154464183185
chr22 51304566 1676280 0.032673115293480895 0.21626043219986396
chrMT 16571 40809 2.4626757588558323 2.2987911879468594
chrX 155270560 6653127 0.042848605685456405 0.2559785364821867
chrY 59373566 679473 0.011444032180920377 0.15175982652678247