BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714059.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 517,250
number of mapped reads = 91,073 (17.61%)
number of supplementary alignments = 1,637 (0.32%)
number of secondary alignments = 0
number of mapped bases = 9,267,397 bp
number of sequenced bases = 9,249,867 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 89,609
duplication rate = 29.15%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 12.8457
>>>>>>> ACTG content
number of A's = 243,015 bp (2.63%)
number of C's = 95,330 bp (1.03%)
number of T's = 130,090 bp (1.41%)
number of G's = 8,781,222 bp (94.93%)
number of N's = 210 bp (0%)
GC percentage = 95.96%
>>>>>>> Mismatches and indels
general error rate = 0.0313
number of mismatches = 225,031
number of insertions = 9,539
mapped reads with insertion percentage = 7.13%
number of deletions = 4,099
mapped reads with deletion percentage = 4.34%
homopolymer indels = 63.57%
>>>>>>> Coverage
mean coverageData = 0.003X
std coverageData = 11.3794X
There is a 0% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% 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 110949 4.451302851518272E-4 0.8005781453698712
chr2 243199373 8775621 0.03608406095685123 40.58335292901666
chr3 198022430 20971 1.0590214451968901E-4 0.0566421883976695
chr4 191154276 7558 3.9538744087524363E-5 0.011224800628306499
chr5 180915260 8202 4.533614245697129E-5 0.010279408454722912
chr6 171115067 9041 5.283579148526997E-5 0.016085799342846225
chr7 159138663 16208 1.0184828560486272E-4 0.10476746832078439
chr8 146364022 6033 4.121914605489592E-5 0.017075700064648175
chr9 141213431 4644 3.288639024711467E-5 0.012815602718483154
chr10 135534747 72870 5.376481058396044E-4 1.011734270107245
chr11 135006516 9797 7.256686780955076E-5 0.03600060218965832
chr12 133851895 17398 1.299794821731885E-4 0.10628077006539702
chr13 115169878 4469 3.8803548962689706E-5 0.015782906422674155
chr14 107349540 12013 1.1190546321856619E-4 0.1225594754577665
chr15 102531392 5649 5.509532144067643E-5 0.019875781974030865
chr16 90354753 5037 5.5746928996640606E-5 0.015153021228895546
chr17 81195210 11079 1.3644893584239759E-4 0.1336524633229196
chr18 78077248 11646 1.4915997039239908E-4 0.06912097082567964
chr19 59128983 4093 6.922155248298453E-5 0.019554961595080852
chr20 63025520 2463 3.9079407833525214E-5 0.01843144065899203
chr21 48129895 1096 2.277170976583265E-5 0.005851509548004757
chr22 51304566 1228 2.3935491433647445E-5 0.005735937769209783
chrMT 16571 2074 0.12515840926920524 0.9972481404974385
chrX 155270560 141056 9.084529610764591E-4 0.15315635857051005
chrY 59373566 6202 1.0445725964985833E-4 0.02463176344539618