Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
592,895 |
A→C |
L103F (TTA→TTC) |
cusF → |
Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 592,895 | 0 | A | C | 92.9%
| 40.9
/ NA
| 14 | L103F (TTA→TTC) | cusF | Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (7/6); total (7/7) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCG > NZ_CP009273/592809‑592977
|
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg > 1:290465/1‑90 (MQ=255)
aCCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGat > 1:402554/1‑90 (MQ=255)
cAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTaaa < 1:100554/90‑1 (MQ=255)
gAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAg < 2:84354/90‑1 (MQ=255)
aaGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGaaaa > 1:111588/1‑90 (MQ=255)
gCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATc < 1:243558/90‑1 (MQ=255)
gTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATcgc < 1:189369/90‑1 (MQ=255)
gTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATc > 2:320731/1‑90 (MQ=255)
gcagGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGgcag > 2:138802/1‑90 (MQ=255)
gcagGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGgcag > 2:281334/1‑90 (MQ=255)
gCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGa > 2:138197/1‑90 (MQ=255)
ctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggcg < 1:281334/90‑1 (MQ=255)
ctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggcg < 2:47863/90‑1 (MQ=255)
ctttATGACAGGATATTCAAGTCAGCCAGTAGCCCAGGTTTAATGAGATGAAAAAAATTGCGCTTATTATCGGCAGCATGATGgcgggcc < 2:324034/90‑2 (MQ=255)
|
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCG > NZ_CP009273/592809‑592977
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC > NZ_CP009273/592799‑592987
|
GCGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAG > SRR3722087.293418/1‑100 (MQ=60)
agatgtgtataagagacagGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGA < SRR3722087.116655/81‑1 (MQ=60)
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGAT > SRR3722087.407222/1‑100 (MQ=60)
CAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGT < SRR3722087.101520/100‑1 (MQ=60)
ACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAA > SRR3722087.112666/1‑100 (MQ=60)
GCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTA < SRR3722087.245878/100‑1 (MQ=60)
GTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATC < SRR3722087.191036/100‑1 (MQ=60)
CTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC < SRR3722087.284134/100‑1 (MQ=60)
|
GCGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC > NZ_CP009273/592799‑592987
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
