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 |
1,972,691 |
A→G |
intergenic (‑237/‑543) |
flhD ← / → uspC |
flagellar transcriptional regulator FlhD/universal stress protein UspC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,972,691 | 0 | A | G | 100.0%
| 35.4
/ NA
| 12 | intergenic (‑237/‑543) | flhD/uspC | flagellar transcriptional regulator FlhD/universal stress protein UspC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (5/7); total (5/7) |
CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACT > NZ_CP009273/1972629‑1972772
|
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGt < 1:266737/90‑1 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTg > 2:153867/1‑90 (MQ=255)
cTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATg > 2:264403/1‑90 (MQ=255)
aaTCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAaca < 2:120404/90‑1 (MQ=255)
tCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac < 1:264403/90‑1 (MQ=255)
cGCAACTGTACTCGTCACGACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt < 2:265307/90‑1 (MQ=255)
aaCTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTAc < 2:95253/90‑1 (MQ=255)
tCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACCCAAAACACTCAATTACTTAAggaa < 1:212850‑M1/90‑5 (MQ=255)
cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg > 2:70548‑M1/1‑80 (MQ=255)
cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > 1:379587‑M1/1‑73 (MQ=255)
cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > 2:70962‑M1/1‑73 (MQ=255)
tACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccct < 2:74565‑M1/90‑22 (MQ=255)
|
CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACT > NZ_CP009273/1972629‑1972772
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTT > NZ_CP009273/1972594‑1972780
|
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGG < SRR3722091.158286/100‑1 (MQ=60)
CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATC < SRR3722091.271065/100‑1 (MQ=60)
TCGACGCAACTGTACTCGTCCCTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTT < SRR3722091.268673/100‑1 (MQ=60)
TCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACCCAAAACACTCAATTACTTAAggaaggtgcgaaca < SRR3722091.216118/100‑15 (MQ=60)
TCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt > SRR3722091.386299/1‑83 (MQ=60)
CTACACGCACATACAAC‑GGGGGGGAGCTGCGATTTTCAATAATGCGGGATGCAGATCACACACAACACTCAATTAtttaatgaaggcggtaacaagtccc > SRR3722091.40196/1‑75 (MQ=60)
GGCACATACAAC‑GCGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACAAAAAACCCTCAATTACTTAAggaaggtgcgaacaagtccctgata > SRR3722091.383569/1‑75 (MQ=60)
CATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACctgtctcttatacacatctgacgctgccgacga > SRR3722091.325519/1‑67 (MQ=60)
|
TAATATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTT > NZ_CP009273/1972594‑1972780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
