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 F1 I1 R1
|
773 |
79.9 |
4112934 |
92.2% |
3792125 |
104.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,767,445 |
(C)7→8 |
intergenic (+90/‑265) |
rnlB → / → yfjP |
CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,767,438 | 1 | . | C | 90.4%
| 158.7
/ 8.5
| 52 | intergenic (+83/‑272) | rnlB/yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| Reads supporting (aligned to +/- strand): ref base . (5/0); new base C (22/25); total (27/25) |
| Fisher's exact test for biased strand distribution p-value = 5.15e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATG > NC_000913/2767303‑2767570
|
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c > 2:1522985/1‑137 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c < 1:1522985/137‑1 (MQ=255)
ctctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑ccc < 1:619356/139‑1 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑Tc < 1:466555/139‑1 (MQ=255)
cGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑Tcc > 1:642928/1‑139 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGa < 2:642928/139‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑Tc < 2:319648/123‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑Tc > 1:319648/1‑123 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTcaca > 1:2011394/1‑117 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTcaca < 2:2011394/117‑1 (MQ=255)
gTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCCCAACG‑TCCTGCATAGGGAACAAGTTTTca > 1:272021/1‑138 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATACGGAACACGTTTTCCCCtgtg > 1:282570/1‑139 (MQ=255)
tttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CACCCCC‑CTCACAACG‑TCCTGCATAAGGAACACGTTTTCCCCTGTGCAc > 1:303362/1‑139 (MQ=255)
ttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCa < 2:282570/139‑1 (MQ=255)
agcttcttTCTAAACGAACCAGTATAGAATTCGCCCTTTTTGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTa < 2:546976/137‑1 (MQ=255)
cttcttTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:218439/129‑1 (MQ=255)
cttcttTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 1:218439/1‑129 (MQ=255)
aCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCtgtg > 1:1906793/1‑114 (MQ=255)
aCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCtgtg < 2:1906793/114‑1 (MQ=255)
aCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCCC‑CCTTCCACGTTCCTACACAGGCATCGCGGTTACTCCGCTGCCTCCCCAACAAAATTTcccccccc > 1:546976/1‑138 (MQ=255)
aaCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa < 2:303362/139‑1 (MQ=255)
ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑C‑CCACC‑CTCACAACA‑GCTAGCATTGGGAACACGTTTTTCCCCAAGCGCCCACGAATAAATTTCCTCTCCTTCaaa > 2:696966/1‑139 (MQ=255)
aGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACt < 2:1770405/139‑1 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAac > 1:896749/1‑83 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAac < 2:896749/83‑1 (MQ=255)
tgtataagagacagATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt < 2:119085/126‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt < 2:272021/139‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGAGAACAAGTTTTTCCCTGTTCACCCACGAATAAATTTCCCACCCTTTACACTTCTCAATAATGt > 1:797934/1‑139 (MQ=255)
gccctttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAAAACATTTTCCCCTGTGCACCCACGCCTAAATTTAACCCCATTTAAACTTCTTAATAATGTc > 2:804753/5‑139 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACATGTTTTCACCTGTGCACCCACCACTAAATTTACCCCCCCTTAAACTTATCAATAATGTCACCAATATTCTGGAAATCCTatg > 2:1884092/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATTAAA‑C‑ACCCC‑CTCACAACA‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCCCGACTAAATCTCGCCCCCTCTAAACTTCCTCATAATTTCACCAAtcttcttttctcttataca > 1:119085/1‑126 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTcaca > 2:1089077/1‑37 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTcaca < 1:1089077/37‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACT‑TCCTCCATAGGGAACACGTTTTCCCCTGTGCACCTACGACTAAATTTCGCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTttga > 2:1849280/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑Tc > 1:1355956/1‑42 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑Tc < 2:1355956/42‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 2:349050/1‑74 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:349050/74‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTCAATTTCCCCCCCTTTAACCTTCTCAATAATGTCACCAATTTTCTGGAAAt > 1:234740/1‑132 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCACTAATGTCACCAATTTTCTGGAAATCCTatga > 1:627830/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAAt < 2:234740/132‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTACCCTGTGCACCCAAGACTAAATTTCTCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga > 2:327638/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCATGCATAGCGAACACGTTTTCCCCAGTGCACCCACGACTAAATTTCCCCACATTTAAACTTCTCAATAATGTCACCAATTTTTTGGAAATCCTatga > 2:288305/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑C‑CCCCCTCTCCCAACG‑TCCTGCATATTGCACACCTTGTCCCCTATCCACCCACGACGAAACTTCCCCCCCTCTAACCTTCACAATCATTTCACCAATCTTCTTGacctactataa > 1:258995/1‑129 (MQ=255)
ccAATATGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatgat < 2:797934/139‑1 (MQ=255)
tatGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCtgt < 1:1381416/64‑1 (MQ=255)
tatGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCtgt > 2:1381416/1‑64 (MQ=255)
atGATCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCtt < 2:258995/139‑1 (MQ=255)
aTCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:477938/81‑1 (MQ=255)
aTCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc > 1:477938/1‑81 (MQ=255)
tCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTtct < 2:1936868/95‑1 (MQ=255)
tCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 2:770338/138‑1 (MQ=255)
tCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc > 1:770338/1‑138 (MQ=255)
tCAAATAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCACCCTTTAAACTtct > 1:1936868/1‑95 (MQ=255)
aaTAGCATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGt < 1:384607/139‑1 (MQ=255)
cATT‑AACC‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATg < 1:327638/139‑1 (MQ=255)
|
CCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑CCCCC‑CTCACAACG‑TCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATG > NC_000913/2767303‑2767570
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
