BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3083750.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,324,165
number of mapped reads = 2,157,870 (92.84%)
number of supplementary alignments = 19,841 (0.85%)
number of secondary alignments = 0
number of mapped bases = 145,183,280 bp
number of sequenced bases = 145,128,457 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 97,365
duplication rate = 3.76%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.5473
>>>>>>> ACTG content
number of A's = 41,154,670 bp (28.36%)
number of C's = 26,004,437 bp (17.92%)
number of T's = 46,802,624 bp (32.25%)
number of G's = 31,143,991 bp (21.46%)
number of N's = 22,735 bp (0.02%)
GC percentage = 39.38%
>>>>>>> Mismatches and indels
general error rate = 0.0077
number of mismatches = 1,096,240
number of insertions = 10,826
mapped reads with insertion percentage = 0.5%
number of deletions = 33,337
mapped reads with deletion percentage = 1.53%
homopolymer indels = 48.75%
>>>>>>> Coverage
mean coverageData = 0.0469X
std coverageData = 0.3932X
There is a 4.01% of reference with a coverageData >= 1X
There is a 0.52% of reference with a coverageData >= 2X
There is a 0.08% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% 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 14084707 0.05650821227041196 0.800821903249849
chr2 243199373 12921820 0.053132620535168894 0.3451920416859967
chr3 198022430 13428823 0.06781465614779093 0.2965050017710841
chr4 191154276 7341699 0.03840719210487345 0.22281091314799384
chr5 180915260 7029690 0.038856257896652834 0.22214391500755654
chr6 171115067 10325028 0.06033967774445017 0.31764781101569384
chr7 159138663 10865868 0.06827924650843649 0.6703650057218439
chr8 146364022 10047795 0.06864935017978667 0.5817520951078002
chr9 141213431 5901605 0.041792094124531255 0.28459284289801906
chr10 135534747 6179850 0.04559605663335912 0.32118616473315303
chr11 135006516 4830001 0.03577605839410003 0.25017048105380785
chr12 133851895 5082827 0.03797351542912411 0.22041094494732125
chr13 115169878 5016223 0.04355499100207434 0.2344788361167245
chr14 107349540 3137888 0.029230567732288375 0.19707282682944516
chr15 102531392 3254298 0.031739528124225605 0.20108391941091694
chr16 90354753 3807041 0.042134374491621926 0.24195293594013087
chr17 81195210 2457158 0.030262351683061108 0.20018427304402478
chr18 78077248 3780303 0.04841747239861733 0.4876917159531904
chr19 59128983 3265802 0.05523183106328752 0.5182486251473387
chr20 63025520 2820481 0.044751411809057666 0.242527462494827
chr21 48129895 2502043 0.05198521625696462 0.2612900054440099
chr22 51304566 1010489 0.01969588827629884 0.1551048609633714
chrMT 16571 9166 0.553134994870557 0.8147442156449771
chrX 155270560 5821819 0.037494673813245734 0.22969296251418575
chrY 59373566 260856 0.004393470319771596 0.10096292849380503