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 |
|
A23 F66 I1 R1
|
33 |
61.7 |
2789148 |
95.4% |
2660847 |
127.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
BS168_reference_genome |
1,317,152 |
+GT |
intergenic (+23/+5) |
phrA → / ← yjpA |
secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | BS168_reference_genome | 1,317,152 | 1 | . | G | 96.2%
| 194.3
/ 0.5
| 54 | intergenic (+23/+5) | phrA/yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base G (25/26); total (28/26) |
| Fisher's exact test for biased strand distribution p-value = 4.91e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.87e-01 |
| * | BS168_reference_genome | 1,317,152 | 2 | . | T | 94.3%
| 150.5
/ 3.2
| 54 | intergenic (+23/+5) | phrA/yjpA | secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme |
| Reads supporting (aligned to +/- strand): ref base . (3/0); new base T (24/26); total (28/26) |
| Fisher's exact test for biased strand distribution p-value = 2.36e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑G‑‑C‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGC > BS168_reference_genome/1317023‑1317273
||
tgCTCGTTGCGGTCGGGTTGAGCTTTTCTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTTCGGCACGCAATCAAACATGATGCAAAAAAAAAGACCCTTAGG‑G‑‑G‑TCtttttt > 1:158574/1‑139 (MQ=255)
cGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑G‑‑G‑TCttttttattt > 8:84656/1‑135 (MQ=255)
gTTCAGCTTTACTCAGGTGATGGGTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCa < 3:126098/139‑1 (MQ=255)
aCTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGTGT‑CTTTTTTATTTCTTCAGCTTCCATTCTTTTATc > 4:225879/1‑139 (MQ=255)
cTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCTGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGATTCCATTCTTTTATCg > 2:308744/1‑139 (MQ=255)
cAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt > 5:90906/1‑138 (MQ=255)
aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt < 7:219382/137‑1 (MQ=255)
aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt < 7:83679/137‑1 (MQ=255)
gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc > 5:259779/1‑139 (MQ=255)
gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc > 6:39044/1‑139 (MQ=255)
gATGGATCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTc < 2:188117/139‑1 (MQ=255)
ggTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCag > 4:30528/1‑138 (MQ=255)
ggTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTC‑TTTTTTATTCTTCAGCTTCCATTCTTTTATCGTCAGCTCag > 3:318641/1‑137 (MQ=255)
cATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCagaaga < 4:158642/138‑1 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGCAGGGAAAACATTACATATATCGGCACGCAATCAAACATGATCCATAAAAAAAGACCCTAAGG‑GGACTTTTTTATTACTTCAGCTTCCATTCTTATATCTTCATATCTGAAGATc > 8:158418/1‑139 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt > 8:275951/1‑125 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt < 7:275951/125‑1 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 6:235073/1‑139 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 7:72008/1‑139 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 3:331771/1‑139 (MQ=255)
aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc > 7:59853/1‑139 (MQ=255)
taaaCAGCAAACACAGCATGGAAAACAATTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGcc < 8:203909/138‑1 (MQ=255)
aaCAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGccac < 7:250252/139‑1 (MQ=255)
aaaCACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTTTTTATTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATACACTTGcccccccccg > 2:173251/1‑134 (MQ=255)
aaCACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGa < 1:173251/139‑1 (MQ=255)
acacAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATCATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGAt < 3:263583/139‑1 (MQ=255)
gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCa > 2:97259/1‑139 (MQ=255)
gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCa < 1:97259/139‑1 (MQ=255)
ttCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATgg < 7:346422/129‑1 (MQ=255)
ttCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATgg > 8:346422/1‑129 (MQ=255)
ttCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCg > 3:181205/1‑139 (MQ=255)
tatTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGc < 3:70112/139‑1 (MQ=255)
tGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt < 4:42025/134‑1 (MQ=255)
tGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt > 3:42025/1‑134 (MQ=255)
gCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctct > 1:264863/1‑139 (MQ=255)
aTCAAACATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAAt < 1:80437/139‑1 (MQ=255)
aCATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCt < 3:116023/139‑1 (MQ=255)
cATGATGCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCtt < 6:63971/139‑1 (MQ=255)
tgattCATAAAAAAAGACCCCTAGG‑GGTCTTTTTTATTTCTTCAGCCTACATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg < 1:308744/139‑1 (MQ=255)
tgatgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg < 3:59375/139‑1 (MQ=255)
tgatgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg < 8:59853/139‑1 (MQ=255)
tgatgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg < 8:72008/139‑1 (MQ=255)
gatgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGa > 1:232735/1‑139 (MQ=255)
gatgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGa > 5:293555/1‑139 (MQ=255)
gatgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGa > 5:236982/1‑139 (MQ=255)
atgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt < 2:158574/139‑1 (MQ=255)
tgCATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGAGCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt > 1:79842/1‑138 (MQ=255)
cATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg > 7:177324/1‑134 (MQ=255)
cATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg < 8:177324/134‑1 (MQ=255)
cATAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGa > 6:126705/1‑138 (MQ=255)
aTAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa < 2:232735/139‑1 (MQ=255)
tAAAAAAAGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATACACTTGCCACCCGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa > 6:332572/1‑138 (MQ=255)
aaaaaaGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATa < 6:236982/138‑1 (MQ=255)
aaaaGACCCTTAGG‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGc < 1:128725/139‑1 (MQ=255)
||
TGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGG‑G‑‑C‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGC > BS168_reference_genome/1317023‑1317273
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
