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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
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%
| 35.9
/ NA
| 11 | 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 (6/5); total (6/5) |
TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCA > NZ_CP009273/1972605‑1972768
|
tACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑gggggg > 2:186754/1‑90 (MQ=255)
aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc < 1:86524/90‑1 (MQ=255)
aGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGc < 2:98956/90‑1 (MQ=255)
acTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGc < 1:186754/90‑1 (MQ=255)
cTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGt < 1:256902/90‑1 (MQ=255)
ttATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTg > 2:144194/1‑90 (MQ=255)
tATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTg > 1:208693/1‑90 (MQ=255)
ttttCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATcac > 1:296376/1‑90 (MQ=255)
tCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt > 1:32427‑M1/1‑83 (MQ=255)
cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg > 1:299076‑M1/1‑80 (MQ=255)
cTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg > 2:265972‑M1/1‑80 (MQ=255)
cacaTACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagt < 2:299076‑M1/90‑18 (MQ=255)
|
TACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCA > NZ_CP009273/1972605‑1972768
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
TGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGT > NZ_CP009273/1972599‑1972784
|
TGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGC < SRR3722090.184305/100‑1 (MQ=60)
AGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAAT < SRR3722090.87476/100‑1 (MQ=60)
TCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTG > SRR3722090.211009/1‑100 (MQ=60)
ACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAACGGGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGA < SRR3722090.188774/100‑1 (MQ=60)
CTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATC < SRR3722090.260044/100‑1 (MQ=60)
TATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCAC > SRR3722090.300121/1‑100 (MQ=60)
gagatgctcaggagtctcgtgggctcggagatgtgtataagagacagCATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACA < SRR3722090.342720/53‑1 (MQ=60)
ACTGTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggt > SRR3722090.32748/1‑93 (MQ=60)
GTACTCGTCACTACACGCACATACAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcg > SRR3722090.302868/1‑90 (MQ=60)
CAAC‑GGGGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAAggaaggtgcgaacaagtccctgatatgagatca > SRR3722090.91028/1‑67 (MQ=60)
|
TGTCCTTACAAATAGAAATGGGTCTTTACACTTATCTAAGATTTTTCCTAAATCGACGCAACTGTACTCGTCACTACACGCACATACAAC‑GGAGGGGGGCTGCGATTTTCAATAATGCGTGATGCAGATCACACAAAACACTCAATTACTTAACATAAATGTATAAGTCATACTTTTGTTTTGGGT > NZ_CP009273/1972599‑1972784
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
