BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081019.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 = 3,358,538
number of mapped reads = 2,724,402 (81.12%)
number of supplementary alignments = 11,671 (0.35%)
number of secondary alignments = 0
number of mapped bases = 168,838,137 bp
number of sequenced bases = 168,778,049 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 94,016
duplication rate = 2.64%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6001
>>>>>>> ACTG content
number of A's = 47,920,935 bp (28.39%)
number of C's = 34,439,100 bp (20.4%)
number of T's = 48,635,069 bp (28.82%)
number of G's = 37,780,864 bp (22.38%)
number of N's = 2,081 bp (0%)
GC percentage = 42.79%
>>>>>>> Mismatches and indels
general error rate = 0.0079
number of mismatches = 1,308,676
number of insertions = 11,676
mapped reads with insertion percentage = 0.43%
number of deletions = 34,870
mapped reads with deletion percentage = 1.27%
homopolymer indels = 45%
>>>>>>> Coverage
mean coverageData = 0.0545X
std coverageData = 0.3945X
There is a 4.63% of reference with a coverageData >= 1X
There is a 0.61% of reference with a coverageData >= 2X
There is a 0.11% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 12885919 0.05169864351110283 0.561453452703394
chr2 243199373 13417563 0.05517104273126559 0.42895829823075493
chr3 198022430 11457062 0.057857395245579 0.27369166435707926
chr4 191154276 10710133 0.05602873879734712 0.28893010062237195
chr5 180915260 11987153 0.0662583852793844 0.2956947521116707
chr6 171115067 9582727 0.05600165530718578 0.3325173241991065
chr7 159138663 9828087 0.061758009114353314 0.7195076064213272
chr8 146364022 9841233 0.0672380607305257 0.4002955123689342
chr9 141213431 6814876 0.04825940388064079 0.3795775437974623
chr10 135534747 8486160 0.06261243103954738 0.36424004557946665
chr11 135006516 7595848 0.05626282512171486 0.3820718855956352
chr12 133851895 6626611 0.049507039104676104 0.2592664186874797
chr13 115169878 5411440 0.046986591407173324 0.24796695487414572
chr14 107349540 5502053 0.05125362437510212 0.279504537103764
chr15 102531392 4660521 0.0454545764871699 0.2639318975188679
chr16 90354753 5001773 0.055357054653228925 0.29781522432515567
chr17 81195210 4576762 0.05636738916002557 0.3081838268396175
chr18 78077248 4929396 0.06313485844173196 0.7326382987004127
chr19 59128983 3423672 0.05790175690997425 0.47445589040754005
chr20 63025520 2979439 0.047273533006947026 0.2552154179911476
chr21 48129895 1961508 0.04075446248116685 0.25332298623821436
chr22 51304566 1893863 0.03691412183469206 0.21880898316087338
chrMT 16571 22505 1.358095467986241 1.4526486343357705
chrX 155270560 8822228 0.056818420697394276 0.3139322369754901
chrY 59373566 419605 0.007067202263040761 0.14458642523848964