BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716781.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 = 4,683,961
number of mapped reads = 3,029,874 (64.69%)
number of supplementary alignments = 68,886 (1.47%)
number of secondary alignments = 0
number of mapped bases = 226,100,397 bp
number of sequenced bases = 226,023,641 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 133,859
duplication rate = 3.1%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.9932
>>>>>>> ACTG content
number of A's = 59,617,826 bp (26.38%)
number of C's = 45,895,937 bp (20.31%)
number of T's = 68,058,369 bp (30.11%)
number of G's = 52,423,557 bp (23.19%)
number of N's = 27,952 bp (0.01%)
GC percentage = 43.5%
>>>>>>> Mismatches and indels
general error rate = 0.0077
number of mismatches = 1,697,589
number of insertions = 18,429
mapped reads with insertion percentage = 0.6%
number of deletions = 44,551
mapped reads with deletion percentage = 1.45%
homopolymer indels = 39.62%
>>>>>>> Coverage
mean coverageData = 0.073X
std coverageData = 0.5458X
There is a 5.83% of reference with a coverageData >= 1X
There is a 1% of reference with a coverageData >= 2X
There is a 0.23% of reference with a coverageData >= 3X
There is a 0.07% of reference with a coverageData >= 4X
There is a 0.03% 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 0.01% 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 17952012 0.0720239409152766 0.6421161674478971
chr2 243199373 19331479 0.0794881942397113 0.8371934208916366
chr3 198022430 15028822 0.07589454386556109 0.3303364691746697
chr4 191154276 14459180 0.07564141541882119 0.3704034925331141
chr5 180915260 13662958 0.075521313127483 0.3376623204138803
chr6 171115067 13025744 0.07612271805381113 0.4009581318674251
chr7 159138663 12459556 0.07829370792187691 0.7245574411576855
chr8 146364022 11641895 0.07954068794310667 0.736894146330521
chr9 141213431 9600788 0.06798778226697147 0.5888529301896369
chr10 135534747 10718795 0.0790852179035683 0.5405017503250877
chr11 135006516 10243905 0.07587711544233909 0.5999579501498378
chr12 133851895 10319833 0.07709889351958746 0.3434070423859411
chr13 115169878 7209038 0.06259482188563228 0.30012147100218445
chr14 107349540 6765066 0.06301904973230439 0.39950637249693133
chr15 102531392 6424993 0.06266366694797239 0.30442478028321446
chr16 90354753 6734181 0.0745304566324253 0.3830818886681487
chr17 81195210 6119250 0.07536466744774722 0.37911891637727135
chr18 78077248 6197594 0.07937772089508073 1.1278287182256566
chr19 59128983 4504771 0.07618549772790782 0.5659705252568648
chr20 63025520 4788270 0.0759735104129248 0.352305060691709
chr21 48129895 2980406 0.061924215708345096 0.34050367689649985
chr22 51304566 2598744 0.050653269340588516 0.27294527516511674
chrMT 16571 5845 0.3527246394303301 0.6631468258707612
chrX 155270560 12769250 0.08223870642316225 0.4806554693702597
chrY 59373566 558022 0.009398492251585495 0.24366158712642702