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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,087,693 |
T→C |
F10F (TTT→TTC) |
rhaS → |
HTH‑type transcriptional activator RhaS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,087,693 | 0 | T | C | 100.0%
| 116.5
/ NA
| 33 | F10F (TTT→TTC) | rhaS | HTH‑type transcriptional activator RhaS |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (27/6); total (27/6) |
ATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAAAT > NZ_CP009273/4087631‑4087776
|
aTTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATa > 2:218574/1‑90 (MQ=255)
aTTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATa > 1:651221/1‑90 (MQ=255)
gCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAAcc > 2:724619/1‑90 (MQ=255)
gCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAAcc > 2:267037/1‑90 (MQ=255)
gtgtTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCg > 1:237947/1‑90 (MQ=255)
tgtTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCgg < 2:517085/90‑1 (MQ=255)
gaggCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt < 1:456341/90‑1 (MQ=255)
ggCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAttt > 2:193463/1‑90 (MQ=255)
gCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAtttt < 1:585373/90‑1 (MQ=255)
aGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCt > 2:492758/1‑90 (MQ=255)
aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat > 2:367763/1‑90 (MQ=255)
aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat < 1:318349/90‑1 (MQ=255)
aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat > 2:152162/1‑90 (MQ=255)
aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat > 2:129449/1‑90 (MQ=255)
aCCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcat > 2:606708/1‑90 (MQ=255)
gTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcat > 1:751863/1‑90 (MQ=255)
aTTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcatca > 2:236753/1‑90 (MQ=255)
aTTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAcatcatca > 2:391221/1‑90 (MQ=255)
tAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGAttt > 2:630862/1‑90 (MQ=255)
tAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGAttt > 1:625689/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGa < 1:686524/73‑1 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGa > 2:686524/1‑73 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 2:409806/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:206520/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 2:102718/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:705981/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:5987/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGCCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:591197/1‑90 (MQ=255)
gtgtGGATTTTTTCCCGCCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAAATCATCATGATTTTc > 2:301838/1‑90 (MQ=255)
gagtgGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTc > 1:677148/3‑90 (MQ=255)
gtgGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCAt > 2:284806/1‑90 (MQ=255)
gATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt < 2:625842/60‑1 (MQ=255)
gATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGAt > 1:625842/1‑60 (MQ=255)
ttttttcCCGTCTGGTAACGCGTCCGTGGCGGTAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAAAt > 2:407653/1‑90 (MQ=255)
|
ATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAAAT > NZ_CP009273/4087631‑4087776
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ 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
GGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAA > NZ_CP009273/4087605‑4087774
|
GGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAA < SRR3722073.644246/100‑1 (MQ=60)
CGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATA > SRR3722073.664601/1‑100 (MQ=60)
CTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCG > SRR3722073.242932/1‑100 (MQ=60)
GAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAAC < SRR3722073.466088/100‑1 (MQ=60)
GCCAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATC < SRR3722073.597599/100‑1 (MQ=60)
CAGTATGACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCAT > SRR3722073.767085/1‑100 (MQ=60)
gagacagGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCAT < SRR3722073.700517/93‑1 (MQ=60)
ACCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATT < SRR3722073.325097/100‑1 (MQ=60)
CCGTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTT > SRR3722073.638672/1‑100 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACtgtctcttatacacatctgacgctgccgacgatatgcagtgtgtagatctcggtggtcgccgta > SRR3722073.104223/1‑36 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCtgtctcttatacacatctgacgctgccgacgatatgcagtgtgtagatctcggtggtcgccg > SRR3722073.352065/1‑38 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722073.6139/1‑100 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722073.720262/1‑100 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722073.210736/1‑100 (MQ=60)
GTATTACATAGTGTGGATTTTTTCCCGCCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722073.603546/1‑100 (MQ=60)
GTATTACATAGAGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTC > SRR3722073.690994/1‑100 (MQ=60)
ATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGctgtctcttatacacatctgacgctgccgacgatggcggtcgtgtagatctcggtgggcgccg > SRR3722073.764979/1‑37 (MQ=60)
ACATAGTGTGGATTTTTTCCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACctgtctcttatacacatctg > SRR3722073.638826/1‑80 (MQ=60)
|
GGTAAGAACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACATCAGGAGGCCAGTATGACCGTATTACATAGTGTGGATTTTTTTCCGTCTGGTAACGCGTCCGTGGCGATAGAACCCCGGCTCCCGCAGGCGGATTTTCCTGAACATCATCATGATTTTCATGAA > NZ_CP009273/4087605‑4087774
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
