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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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%
| 77.5
/ NA
| 24 | 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 (8/16); total (8/16) |
TTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG > NZ_CP009273/1972604‑1972776
|
ttACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGgggg < 1:242872/90‑1 (MQ=255)
aaaTAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGgggggggg > 1:212525/1‑90 (MQ=255)
aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGc < 1:464325/90‑1 (MQ=255)
gggTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGAtttt < 1:266692/90‑1 (MQ=255)
ttACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCaataa < 2:37298/90‑1 (MQ=255)
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGt < 2:292823/90‑1 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg > 2:337437/1‑90 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg > 2:280277/1‑90 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTg > 2:150122/1‑90 (MQ=255)
tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGa > 2:3591/1‑90 (MQ=255)
tttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcaca > 1:18567/1‑90 (MQ=255)
aTCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAacac < 1:3591/90‑1 (MQ=255)
cGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAt < 1:280277/90‑1 (MQ=255)
gCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt < 2:333535/90‑1 (MQ=255)
gCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt < 2:212525/90‑1 (MQ=255)
aCTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt < 1:152977/82‑1 (MQ=255)
aCTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAAtt > 2:152977/1‑82 (MQ=255)
tCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaa < 1:134433‑M1/90‑5 (MQ=255)
cACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtg < 1:213453‑M1/90‑9 (MQ=255)
cacGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaac < 1:182908‑M1/90‑14 (MQ=255)
cacaTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt < 1:228985‑M1/90‑18 (MQ=255)
aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGc > 1:451284/1‑42 (MQ=255)
aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGc < 2:451284/42‑1 (MQ=255)
aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc < 1:340273‑M1/90‑21 (MQ=255)
aTACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccc < 2:401055‑M1/90‑21 (MQ=255)
aCGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata > 1:97441‑M1/1‑65 (MQ=255)
|
TTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTG > NZ_CP009273/1972604‑1972776
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
ATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTG > NZ_CP009273/1972598‑1972781
|
ATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGG > SRR3722094.215388/1‑100 (MQ=60)
TTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGA < SRR3722094.246368/100‑1 (MQ=60)
AGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAAT < SRR3722094.472498/100‑1 (MQ=60)
GGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCG < SRR3722094.270667/100‑1 (MQ=60)
ATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACA > SRR3722094.18845/1‑100 (MQ=60)
ATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTT < SRR3722094.3648/100‑1 (MQ=60)
CGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAgga < SRR3722094.284489/100‑4 (MQ=60)
GCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaa < SRR3722094.155110/100‑5 (MQ=60)
TCGTCACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaaca < SRR3722094.136356/100‑15 (MQ=60)
CACTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtc < SRR3722094.216327/100‑19 (MQ=60)
CTACACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACActgtctcttatacacatctgacgctgccgacgaccatc > SRR3722094.459219/1‑62 (MQ=60)
CACGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctga < SRR3722094.185417/100‑24 (MQ=60)
CGCACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgata > SRR3722094.98850/1‑75 (MQ=60)
CACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatg < SRR3722094.232136/100‑28 (MQ=60)
CACATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatg > SRR3722094.201494/1‑73 (MQ=60)
CATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgactgtct > SRR3722094.199935/1‑71 (MQ=60)
ATACAACGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgaga < SRR3722094.345883/100‑31 (MQ=60)
|
ATGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTG > NZ_CP009273/1972598‑1972781
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
