BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3084875.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 = 2,575,290
number of mapped reads = 2,333,063 (90.59%)
number of supplementary alignments = 17,019 (0.66%)
number of secondary alignments = 0
number of mapped bases = 163,518,108 bp
number of sequenced bases = 163,454,987 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 99,724
duplication rate = 3.44%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 48.0137
>>>>>>> ACTG content
number of A's = 48,134,854 bp (29.45%)
number of C's = 30,045,879 bp (18.38%)
number of T's = 52,307,039 bp (32%)
number of G's = 32,940,080 bp (20.15%)
number of N's = 27,135 bp (0.02%)
GC percentage = 38.53%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 1,336,904
number of insertions = 13,000
mapped reads with insertion percentage = 0.55%
number of deletions = 35,933
mapped reads with deletion percentage = 1.52%
homopolymer indels = 48.12%
>>>>>>> Coverage
mean coverageData = 0.0528X
std coverageData = 0.4698X
There is a 4.44% of reference with a coverageData >= 1X
There is a 0.64% of reference with a coverageData >= 2X
There is a 0.1% 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 12683594 0.05088691032789844 0.9440652331413042
chr2 243199373 12711051 0.05226596945214986 0.43483035552856736
chr3 198022430 13354914 0.06744142065118583 0.29680111668444387
chr4 191154276 9491497 0.04965359498418963 0.2549916760359337
chr5 180915260 8599422 0.047532872572496096 0.2595909357716698
chr6 171115067 9885892 0.057773357853987226 0.28447690773996465
chr7 159138663 8216789 0.05163288948833258 0.3441922723727737
chr8 146364022 10431470 0.07127072526061083 1.0030346414864049
chr9 141213431 12014138 0.0850778705320176 0.47040378885417744
chr10 135534747 5375684 0.0396627737092393 0.2904313663016306
chr11 135006516 6848776 0.05072922554345451 0.33965893720774804
chr12 133851895 7592723 0.05672480766895381 0.2762890145279281
chr13 115169878 4282180 0.0371814234274 0.21794547457931057
chr14 107349540 3063010 0.02853305193482897 0.2157330874033041
chr15 102531392 3486673 0.03400590718596701 0.20865263602771075
chr16 90354753 3020217 0.03342621057245323 0.24935931887160198
chr17 81195210 4517620 0.055638996438336696 0.27747053980003467
chr18 78077248 6971650 0.08929169737130078 0.8116745634391914
chr19 59128983 3061211 0.05177175125775459 0.5466996175645968
chr20 63025520 3072725 0.048753663595318214 0.26517416848658965
chr21 48129895 1386819 0.02881408737750207 0.20868811107249335
chr22 51304566 1294314 0.02522804695394948 0.17693497777963857
chrMT 16571 38077 2.2978094261058475 1.8173839431338843
chrX 155270560 11778824 0.07585999561024317 0.3461120934860932
chrY 59373566 338838 0.005706883093395469 0.1392449350324837