BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6068069.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 = 4,681,421
number of mapped reads = 4,357,668 (93.08%)
number of supplementary alignments = 37,969 (0.81%)
number of secondary alignments = 0
number of mapped bases = 281,713,619 bp
number of sequenced bases = 281,605,982 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 915,712
duplication rate = 15.66%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7823
>>>>>>> ACTG content
number of A's = 72,515,710 bp (25.75%)
number of C's = 51,159,233 bp (18.17%)
number of T's = 91,251,956 bp (32.4%)
number of G's = 66,647,085 bp (23.67%)
number of N's = 31,998 bp (0.01%)
GC percentage = 41.83%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 1,508,412
number of insertions = 18,947
mapped reads with insertion percentage = 0.43%
number of deletions = 61,571
mapped reads with deletion percentage = 1.4%
homopolymer indels = 44.47%
>>>>>>> Coverage
mean coverageData = 0.091X
std coverageData = 1.0044X
There is a 5.17% of reference with a coverageData >= 1X
There is a 2.06% of reference with a coverageData >= 2X
There is a 0.9% of reference with a coverageData >= 3X
There is a 0.41% of reference with a coverageData >= 4X
There is a 0.19% of reference with a coverageData >= 5X
There is a 0.09% of reference with a coverageData >= 6X
There is a 0.05% of reference with a coverageData >= 7X
There is a 0.03% of reference with a coverageData >= 8X
There is a 0.02% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% 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 36426380 0.1461435877425557 1.9587178630626019
chr2 243199373 28954229 0.11905552486765662 1.835797129693588
chr3 198022430 13030391 0.0658026012507775 0.4080193214324123
chr4 191154276 13376879 0.0699794913298199 0.48045533140883523
chr5 180915260 14368839 0.07942303485068092 0.4460843194213743
chr6 171115067 19923165 0.11643138941119661 0.7225245316625805
chr7 159138663 21194457 0.13318232414708675 1.4489382167983447
chr8 146364022 12163486 0.08310434377103958 1.2048030797139349
chr9 141213431 7288111 0.05161060777568672 0.5654715945404518
chr10 135534747 11515996 0.08496711179163524 0.6049962350179064
chr11 135006516 12003081 0.0889074198463132 0.5712140521989694
chr12 133851895 12319227 0.09203625395068184 0.4935545374638817
chr13 115169878 9471671 0.08224087030811998 0.5176086515186935
chr14 107349540 4275209 0.0398251264048267 0.34564290507402484
chr15 102531392 5813699 0.056701648993510205 0.4102358063600879
chr16 90354753 7272337 0.08048649084348668 0.47083812335989095
chr17 81195210 7881015 0.09706256071016997 0.5178014976834531
chr18 78077248 6754532 0.08651088726897752 1.1970028381097368
chr19 59128983 7649309 0.12936649020329 1.277274336035589
chr20 63025520 4338842 0.0688426212112173 0.4446692252077531
chr21 48129895 3338260 0.06935938671796396 0.4552300963880578
chr22 51304566 3123496 0.06088144279400005 0.3856651788370328
chrMT 16571 138895 8.381811598575824 6.856738355665158
chrX 155270560 18158167 0.11694533078260295 0.6428966125137868
chrY 59373566 933946 0.015729996746363526 0.5291720454042005