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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
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 | 100.0%
| 39.8
/ NA
| 13 | L103F (TTA→TTC) | cusF | Cu(+)/Ag(+) efflux RND transporter periplasmic metallochaperone CusF |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (6/7); total (6/7) |
GCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCG > NZ_CP009273/592817‑592977
|
gCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTaa > 2:272584/1‑90 (MQ=255)
gACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGt > 2:315262/1‑90 (MQ=255)
gAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAg < 1:315262/90‑1 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg < 1:70499/54‑1 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAg > 2:70499/1‑54 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATgag > 2:202347/1‑90 (MQ=255)
ggCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATgag > 2:2422/1‑90 (MQ=255)
gCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATc < 1:202347/90‑1 (MQ=255)
gCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATc < 2:71951/90‑1 (MQ=255)
tAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCt < 2:130880/90‑1 (MQ=255)
tCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCg < 1:272584/90‑1 (MQ=255)
gCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGa > 2:352451/1‑90 (MQ=255)
ctttATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCgcgggcg < 2:92394/90‑1 (MQ=255)
|
GCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCG > NZ_CP009273/592817‑592977
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATT > NZ_CP009273/592800‑592985
|
AGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGG < SRR3722091.413733/100‑1 (MQ=60)
CTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGAT < SRR3722091.303126/100‑1 (MQ=60)
cagcgtcagatgtgtataagagacagAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAG < SRR3722091.71575/74‑1 (MQ=60)
GAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCC < SRR3722091.320680/100‑1 (MQ=60)
GCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTA < SRR3722091.205404/100‑1 (MQ=60)
TCCAGCAGGGCAACCTTTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGAT < SRR3722091.277068/100‑1 (MQ=60)
TTCTTTATTCCAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATT > SRR3722091.144210/1‑100 (MQ=60)
|
CGCTTTACCATCACCCCGCAGACGAAAATGAGTGAAATTAAAACCGGCGACAAAGTGGCGTTTAATTTTGTCCAGCAGGGCAACCTTTCTTTATTACAGGATATTAAAGTCAGCCAGTAACCCAGGTTTAATGAGATGAAAAAAATCGCGCTTATTATCGGCAGCATGATCGCGGGCGGTATTATT > NZ_CP009273/592800‑592985
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
