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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 94.7%
| 58.1
/ ‑3.3
| 19 | 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 (9/9); total (9/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.31e-01 |
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCG > NZ_CP009273/592809‑592977
|
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg < 2:301355/90‑1 (MQ=255)
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg < 1:446696/90‑1 (MQ=255)
aCCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGat > 1:480826/1‑90 (MQ=255)
gCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGTATATTaa > 1:642175/1‑90 (MQ=255)
gACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGa < 1:221254/81‑1 (MQ=255)
gACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGa > 2:221254/1‑81 (MQ=255)
tGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTCTATTCCAGGATATTAAAGTCAGCCAGt < 1:443746/90‑1 (MQ=255)
gAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTa < 1:574664/90‑1 (MQ=255)
aGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTaa > 2:369888/1‑90 (MQ=255)
gAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAAccc < 1:276318/90‑1 (MQ=255)
gAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAAccc < 1:72486/90‑1 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATgag > 1:416388/1‑90 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATgag > 1:179426/1‑90 (MQ=255)
aTTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCtta > 1:273209/1‑90 (MQ=255)
gTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATc > 2:305764/1‑90 (MQ=255)
aCCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATcg > 1:282604/1‑90 (MQ=255)
ctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggcg < 1:379845/90‑1 (MQ=255)
ctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggcg < 1:369888/90‑1 (MQ=255)
ctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggcg < 2:27190/90‑1 (MQ=255)
|
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCG > NZ_CP009273/592809‑592977
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ 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
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC > NZ_CP009273/592802‑592987
|
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGAT < SRR3722112.22699/100‑1 (MQ=60)
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGAT < SRR3722112.597803/100‑1 (MQ=60)
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGAT > SRR3722112.487714/1‑100 (MQ=60)
CCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGTATATTAA > SRR3722112.652164/1‑100 (MQ=60)
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAG < SRR3722112.452913/100‑1 (MQ=60)
CACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTC < SRR3722112.223913/100‑1 (MQ=60)
TGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTCTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTT < SRR3722112.449899/100‑1 (MQ=60)
GAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTT < SRR3722112.583426/100‑1 (MQ=60)
GAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATG < SRR3722112.279543/100‑1 (MQ=60)
GAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATG < SRR3722112.73366/100‑1 (MQ=60)
AATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAG > SRR3722112.421883/1‑100 (MQ=60)
AATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAG > SRR3722112.181620/1‑100 (MQ=60)
GTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTA > SRR3722112.276401/1‑100 (MQ=60)
CAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCG > SRR3722112.285885/1‑100 (MQ=60)
CCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCctgtctcttatacacatctga > SRR3722112.592847/1‑79 (MQ=60)
CTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC < SRR3722112.384773/100‑1 (MQ=60)
CTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC < SRR3722112.374669/100‑1 (MQ=60)
|
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTC > NZ_CP009273/592802‑592987
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
