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 |
|
A9 F1 I2 R1
|
760 |
52.7 |
2744488 |
90.2% |
2475528 |
105.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,190,061 |
(G)6→7 |
coding (387/672 nt) |
phoP ← |
response regulator in two‑component regulatory system with PhoQ |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,190,055 | 1 | . | G | 98.0%
| 168.2
/ ‑3.4
| 49 | coding (393/672 nt) | phoP | response regulator in two‑component regulatory system with PhoQ |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (25/23); total (26/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.38e-01 |
ACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTT > NC_000913/1189942‑1190182
|
aCCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGaa > 1:842744/1‑139 (MQ=255)
tttCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATg < 1:471595/139‑1 (MQ=255)
taataGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCa > 1:49961/1‑139 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGaa < 2:1200681/87‑1 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGaa > 1:1200681/1‑87 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc > 2:1366544/1‑101 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc < 1:1366544/101‑1 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg > 2:996738/1‑139 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg > 1:588958/1‑139 (MQ=255)
tgtATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTcgcg > 2:802207/1‑139 (MQ=255)
tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc > 1:625503/1‑99 (MQ=255)
tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc < 2:625503/99‑1 (MQ=255)
tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGcc > 1:243658/1‑139 (MQ=255)
tATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGcc < 1:802207/139‑1 (MQ=255)
aTTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc < 1:213952/98‑1 (MQ=255)
aTTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGc > 2:213952/1‑98 (MQ=255)
ttCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAt < 2:49961/139‑1 (MQ=255)
cGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCa < 2:588958/139‑1 (MQ=255)
gAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAc < 2:243658/139‑1 (MQ=255)
aCGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACct > 1:707553/1‑139 (MQ=255)
cgcgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAcc > 1:277452/1‑137 (MQ=255)
cgcgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAcc < 2:277452/137‑1 (MQ=255)
cgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAc > 2:1123750/1‑134 (MQ=255)
cgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCAc < 1:1123750/134‑1 (MQ=255)
cgGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCtt < 2:842744/139‑1 (MQ=255)
ttGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGa < 2:1053605/139‑1 (MQ=255)
cACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACgg > 1:1336553/1‑139 (MQ=255)
cTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGtt > 2:327188/1‑139 (MQ=255)
tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgcc < 1:411977/89‑1 (MQ=255)
tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgcc > 2:411977/1‑89 (MQ=255)
tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAt < 2:552895/114‑1 (MQ=255)
tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCAt > 1:552895/1‑114 (MQ=255)
tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑ggggggga > 1:827078/1‑51 (MQ=255)
tCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑ggggggga < 2:827078/53‑3 (MQ=255)
cATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTAt < 2:1063777/79‑1 (MQ=255)
cATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTAt > 1:1063777/1‑79 (MQ=255)
ttAATAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTcaca < 2:1336553/139‑1 (MQ=255)
aTAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGa < 2:118595/53‑1 (MQ=255)
aTAGATAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGa > 1:118595/1‑53 (MQ=255)
aTAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAat > 2:140408/1‑139 (MQ=255)
aTAATTCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAatcat > 2:527549/1‑139 (MQ=255)
ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTc > 1:162472/1‑125 (MQ=255)
ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTc < 2:162472/125‑1 (MQ=255)
ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATa > 2:960827/1‑130 (MQ=255)
ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATa < 1:960827/130‑1 (MQ=255)
ttCACGGCGAGAGAGATCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGc > 2:459997/1‑139 (MQ=255)
agagaTCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgccg > 1:1342895/1‑62 (MQ=255)
agagaTCAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTAcgccg < 2:1342895/62‑1 (MQ=255)
cAACCTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACtt < 2:707553/139‑1 (MQ=255)
ccTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGaa < 2:1149743/94‑1 (MQ=255)
ccTGAAACGGGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGaa > 1:1149743/1‑94 (MQ=255)
|
ACCACTTTGCCATTATTGCGTATCAACGTTTCCATAATAGTGTATTCGAACGCGGTCAGTTTGATCACTTCGTCATTAATAGATAATTCACGGCGAGAGAGATCAACCTGAAAC‑GGGGGGAGCGAAATGACCTGTGAAGCCAGACCGCTATTACGCCGCATTAATGCCTGCATTCGCGCCATCACCTCTTCAATATGAAACGGTTTAGTCACATAATCATCAGCACCGGCACTTAATACTT > NC_000913/1189942‑1190182
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
