BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472720.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 46,630
number of mapped reads = 45,898 (98.43%)
number of supplementary alignments = 166 (0.36%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 23,163
number of mapped paired reads (second in pair) = 22,735
number of mapped paired reads (both in pair) = 45,368
number of mapped paired reads (singletons) = 530
number of mapped bases = 4,519,089 bp
number of sequenced bases = 4,518,524 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 8,776
duplication rate = 19.24%
>>>>>>> Insert size
mean insert size = 29,088.5675
std insert size = 1,383,780.8034
median insert size = 235
>>>>>>> Mapping quality
mean mapping quality = 54.3253
>>>>>>> ACTG content
number of A's = 1,236,551 bp (27.37%)
number of C's = 1,029,714 bp (22.79%)
number of T's = 1,230,262 bp (27.23%)
number of G's = 1,021,074 bp (22.6%)
number of N's = 923 bp (0.02%)
GC percentage = 45.39%
>>>>>>> Mismatches and indels
general error rate = 0.0063
number of mismatches = 27,916
number of insertions = 243
mapped reads with insertion percentage = 0.51%
number of deletions = 239
mapped reads with deletion percentage = 0.52%
homopolymer indels = 46.89%
>>>>>>> Coverage
mean coverageData = 0.0015X
std coverageData = 0.0618X
There is a 0.09% of reference with a coverageData >= 1X
There is a 0.03% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0.01% 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 485514 0.001947894845967104 0.07992703390073039
chr2 243199373 290698 0.0011953073579675717 0.0554402819298187
chr3 198022430 503847 0.0025443935820805754 0.07925178502568635
chr4 191154276 163609 8.559002886234154E-4 0.045702759214530084
chr5 180915260 225423 0.0012460142942060277 0.052874868786921686
chr6 171115067 275378 0.0016093147425761168 0.06306171500243914
chr7 159138663 190372 0.0011962649202350028 0.054405014772987675
chr8 146364022 212750 0.0014535675987367989 0.061894037107610524
chr9 141213431 314106 0.002224335162566796 0.07961603724010148
chr10 135534747 119462 8.814123510334955E-4 0.04529383301824104
chr11 135006516 213143 0.001578760835514043 0.06386791784484296
chr12 133851895 246918 0.0018447105287526934 0.0679505091972152
chr13 115169878 89739 7.791881137531464E-4 0.04467253672419384
chr14 107349540 122790 0.0011438334994262668 0.06289339319308195
chr15 102531392 109904 0.0010719058607923707 0.05177023554646853
chr16 90354753 157499 0.001743118040508616 0.06613980635843943
chr17 81195210 177615 0.002187505888586285 0.07169398645605977
chr18 78077248 89801 0.001150155804671804 0.06071391164013063
chr19 59128983 99679 0.001685789183960766 0.06200671162490704
chr20 63025520 95312 0.001512276296966689 0.06135220422827702
chr21 48129895 25309 5.258478124666592E-4 0.03505681581144606
chr22 51304566 60827 0.001185605975109506 0.05191096345860711
chrMT 16571 577 0.03481986603101804 0.19879987175782807
chrX 155270560 237803 0.001531539526874895 0.06005320677204379
chrY 59373566 11014 1.85503427569097E-4 0.019272883708748637