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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,760,505 |
(T)5→4 |
coding (2438/3057 nt) |
ydiJ ← |
FAD‑binding and (Fe‑S)‑binding domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,760,501 | 0 | T | . | 100.0%
| 109.1
/ NA
| 27 | coding (2442/3057 nt) | ydiJ | FAD‑binding and (Fe‑S)‑binding domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (11/16); total (11/16) |
AAAACGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAATTTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACTGT > NZ_CP009273/1760423‑1760581
|
aaaaCGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGa < 2:873600/90‑1 (MQ=255)
aaaCGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGAc < 1:566653/90‑1 (MQ=255)
aaaCGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGAc < 2:171341/90‑1 (MQ=255)
aGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAAt < 1:763652/90‑1 (MQ=255)
aaCCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGc > 2:199629/1‑90 (MQ=255)
ccTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGcca > 2:289185/1‑90 (MQ=255)
tttAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGccacc < 2:318185/90‑1 (MQ=255)
atGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑gc > 2:248003/1‑90 (MQ=255)
gCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑gcgc < 1:113128/90‑1 (MQ=255)
gCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑gcgc > 2:314322/1‑90 (MQ=255)
gCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑gcgc > 1:65207/1‑90 (MQ=255)
gCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑gcgc > 1:72026/1‑90 (MQ=255)
gggCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCTTc > 2:904240/1‑90 (MQ=255)
gCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAg < 1:199629/90‑1 (MQ=255)
ccATTTGGCGAAAATGGCAGTAACACAGGCTGGAATCCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGc < 2:397902/90‑1 (MQ=255)
aTTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTg > 1:181715/1‑90 (MQ=255)
aTTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TCTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTg < 2:721202/90‑1 (MQ=255)
gCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCGCATCGTAATAGCTGGTAAAGGGGTcc < 2:802666/90‑1 (MQ=255)
cAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGc < 1:307417/90‑1 (MQ=255)
aGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAACTCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGca < 1:175443/90‑1 (MQ=255)
aGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGca < 2:785667/90‑1 (MQ=255)
tAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGcacc < 1:289185/90‑1 (MQ=255)
tAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGcacc < 2:65207/90‑1 (MQ=255)
aGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAac > 2:217216/1‑90 (MQ=255)
ggCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAaca > 2:357836/1‑90 (MQ=255)
gCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAacac < 2:181715/90‑1 (MQ=255)
ggAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACtgt > 1:887016/1‑90 (MQ=255)
|
AAAACGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAATTTTTCGACCAGACGGACAAAATCCGCCACCACTT‑‑GCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACTGT > NZ_CP009273/1760423‑1760581
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 30 ≤ 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
AAACGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAATTTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACTGT > NZ_CP009273/1760424‑1760581
|
AAACGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATC < SRR3722072.576797/100‑1 (MQ=60)
AGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCAC < SRR3722072.777108/100‑1 (MQ=60)
CCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGC > SRR3722072.66406/1‑100 (MQ=60)
CCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGC > SRR3722072.73366/1‑100 (MQ=60)
GCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAG < SRR3722072.115213/100‑1 (MQ=60)
GGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTG > SRR3722072.184859/1‑100 (MQ=60)
GCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGG < SRR3722072.203073/100‑1 (MQ=60)
CAGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACA < SRR3722072.312750/100‑1 (MQ=60)
AGTAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAACTCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACAC < SRR3722072.178475/100‑1 (MQ=60)
TAACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACTG < SRR3722072.294179/100‑1 (MQ=60)
AACACAGGCTGGAAACCTAA‑TTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACTGT > SRR3722072.902273/1‑100 (MQ=60)
|
AAACGATTAAGAAAACCTTTAATATGCTGGGCTTTGCCATTTGGCGAAAATGGCAGTAACACAGGCTGGAAACCTAATTTTTCGACCAGACGGACAAAATCCGCCACCACTTGCGCATCGTAATAGCTGGTAAAGGGGTCCTGCACCACCAACACTGT > NZ_CP009273/1760424‑1760581
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
