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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
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 | 86.7%
| 39.2
/ 0.1
| 15 | L103F (TTA→TTC) | cusF | Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF |
| Reads supporting (aligned to +/- strand): ref base A (0/2); new base C (6/7); total (6/9) |
| Fisher's exact test for biased strand distribution p-value = 4.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.90e-01 |
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGC > NZ_CP009273/592809‑592976
|
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg < 1:333384/90‑1 (MQ=255)
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg < 1:369249/90‑1 (MQ=255)
aTCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg < 2:551346/90‑1 (MQ=255)
cGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTa > 1:462206/1‑90 (MQ=255)
gCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTaa > 1:97797/1‑90 (MQ=255)
aCGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTc < 1:43155/90‑1 (MQ=255)
cGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCa < 1:144584/90‑1 (MQ=255)
gAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAAccc < 2:430119/90‑1 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATgag > 2:88874/1‑90 (MQ=255)
gCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATc > 1:274242/1‑90 (MQ=255)
gTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATcgc < 2:462206/90‑1 (MQ=255)
gTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATc > 2:181917/1‑90 (MQ=255)
gggCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCAt < 1:478309/90‑1 (MQ=255)
aCCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATcg < 1:181917/90‑1 (MQ=255)
tctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggc > 1:161212/1‑90 (MQ=255)
|
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGC > NZ_CP009273/592809‑592976
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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
CATGCGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTCTG > NZ_CP009273/592796‑592989
|
CATGCGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTC < SRR3722109.481889/100‑1 (MQ=60)
ACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTA > SRR3722109.469143/1‑100 (MQ=60)
CCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAA > SRR3722109.99008/1‑100 (MQ=60)
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAG < SRR3722109.337798/100‑1 (MQ=60)
ATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAG < SRR3722109.374428/100‑1 (MQ=60)
ACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAAC < SRR3722109.43666/100‑1 (MQ=60)
CGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACC < SRR3722109.146371/100‑1 (MQ=60)
CGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATC > SRR3722109.277683/1‑100 (MQ=60)
GGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGC > SRR3722109.163209/1‑100 (MQ=60)
GGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGC < SRR3722109.485517/100‑1 (MQ=60)
ACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTAT < SRR3722109.184155/100‑1 (MQ=60)
TCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTT > SRR3722109.413901/1‑100 (MQ=60)
TTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTCTG > SRR3722109.237277/1‑100 (MQ=60)
|
CATGCGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATTTCTG > NZ_CP009273/592796‑592989
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
