BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714231.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 = 248,334
number of mapped reads = 50,379 (20.29%)
number of supplementary alignments = 1,923 (0.77%)
number of secondary alignments = 0
number of mapped bases = 5,540,203 bp
number of sequenced bases = 5,472,452 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 45,792
duplication rate = 50.26%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 37.1352
>>>>>>> ACTG content
number of A's = 781,651 bp (14.28%)
number of C's = 639,981 bp (11.69%)
number of T's = 714,158 bp (13.05%)
number of G's = 3,336,577 bp (60.97%)
number of N's = 85 bp (0%)
GC percentage = 72.67%
>>>>>>> Mismatches and indels
general error rate = 0.0351
number of mismatches = 165,613
number of insertions = 4,340
mapped reads with insertion percentage = 6.18%
number of deletions = 9,011
mapped reads with deletion percentage = 17.21%
homopolymer indels = 39.83%
>>>>>>> Coverage
mean coverageData = 0.0018X
std coverageData = 3.3449X
There is a 0.01% of reference with a coverageData >= 1X
There is a 0.01% 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 95950 3.849539054909717E-4 0.15183318369401383
chr2 243199373 2855183 0.011740091945056125 11.88172827065048
chr3 198022430 62217 3.1419168020511615E-4 0.07014355908878665
chr4 191154276 49644 2.597064582536464E-4 0.07181316461474242
chr5 180915260 64649 3.5734409579379873E-4 0.08983187466134486
chr6 171115067 78524 4.588958843700187E-4 0.15976932876256675
chr7 159138663 87864 5.521222708776936E-4 0.2096742771505119
chr8 146364022 160052 0.0010935201001787175 0.5112268784558198
chr9 141213431 34126 2.416625653688706E-4 0.09094159616012909
chr10 135534747 48944 3.6111772872531354E-4 0.20380513609015635
chr11 135006516 47372 3.508867675690557E-4 0.08268441664560026
chr12 133851895 62611 4.6776326924620676E-4 0.11710972839807048
chr13 115169878 17360 1.507338576845588E-4 0.035687298753494585
chr14 107349540 52778 4.916462613626477E-4 0.16111967556031997
chr15 102531392 34318 3.347072475130348E-4 0.0698773682682381
chr16 90354753 39133 4.3310394528996165E-4 0.11473477998293993
chr17 81195210 77978 9.603768498166333E-4 0.24945530673466285
chr18 78077248 13942 1.7856674456558715E-4 0.037971170069298
chr19 59128983 28640 4.8436483340158243E-4 0.11810160112083683
chr20 63025520 71334 0.0011318272344282125 0.40377497958636643
chr21 48129895 9648 2.0045753268316916E-4 0.033156614923006866
chr22 51304566 6298 1.227571050888531E-4 0.03463475661541688
chrMT 16571 392 0.02365578420131555 0.4282244683769284
chrX 155270560 1534029 0.009879715768398079 1.1694189526139163
chrY 59373566 7217 1.2155240936682159E-4 0.029142220949165066