BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714143.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 = 714,372
number of mapped reads = 572,501 (80.14%)
number of supplementary alignments = 15,846 (2.22%)
number of secondary alignments = 0
number of mapped bases = 74,634,309 bp
number of sequenced bases = 72,889,413 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 515,827
duplication rate = 44.04%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 51.7723
>>>>>>> ACTG content
number of A's = 19,471,071 bp (26.71%)
number of C's = 15,924,372 bp (21.85%)
number of T's = 18,456,085 bp (25.32%)
number of G's = 19,037,347 bp (26.12%)
number of N's = 538 bp (0%)
GC percentage = 47.97%
>>>>>>> Mismatches and indels
general error rate = 0.0454
number of mismatches = 3,107,227
number of insertions = 75,556
mapped reads with insertion percentage = 12.7%
number of deletions = 270,363
mapped reads with deletion percentage = 44.72%
homopolymer indels = 29.06%
>>>>>>> Coverage
mean coverageData = 0.0241X
std coverageData = 7.4442X
There is a 0.05% of reference with a coverageData >= 1X
There is a 0.03% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.02% of reference with a coverageData >= 8X
There is a 0.02% of reference with a coverageData >= 9X
There is a 0.02% 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 0.01% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 6021260 0.02415745234993818 5.251377296263653
chr2 243199373 9592159 0.039441544941812 13.396252452758894
chr3 198022430 2331542 0.011774130839622561 1.9647373821226533
chr4 191154276 2477816 0.012962388557815991 2.6361839828589875
chr5 180915260 3713660 0.02052706886085784 3.5592931694653713
chr6 171115067 2829133 0.01653351192037344 3.6726724327950246
chr7 159138663 2215794 0.0139236685682096 2.289190942782684
chr8 146364022 3084333 0.021073027085850373 4.992973497664677
chr9 141213431 2797297 0.019809001029087666 3.903818157562667
chr10 135534747 3828704 0.028248874069171353 5.086996300215774
chr11 135006516 3369543 0.024958373120301837 3.909772422367649
chr12 133851895 3785583 0.028281878265526236 5.3886775102967315
chr13 115169878 2616402 0.022717763059538883 7.1137852847142575
chr14 107349540 5225181 0.04867446101771838 26.974950348289827
chr15 102531392 2585935 0.025220909904353977 4.5862881672488856
chr16 90354753 1526649 0.01689616704502529 2.406531660342957
chr17 81195210 3103971 0.038228498947166956 6.731808962875721
chr18 78077248 1710829 0.02191200437802316 4.777800848655828
chr19 59128983 1729099 0.029242833417243114 3.6002277532801688
chr20 63025520 2072087 0.03287695206640104 5.203149071542015
chr21 48129895 674221 0.014008362162435634 2.3339542112811698
chr22 51304566 389987 0.007601409200109012 0.8977167028576442
chrMT 16571 151104 9.118580652947921 74.34181906792207
chrX 155270560 6192909 0.03988463105948739 4.452606375788897
chrY 59373566 609111 0.010258959349014003 1.9097313069729813