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 |
|
A4 F1 I2 R1
|
780 |
68.3 |
3343050 |
93.5% |
3125751 |
102.9 |
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 | 87.7%
| 171.8
/ 14.2
| 57 | 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 . (7/0); new base C (22/28); total (29/28) |
| Fisher's exact test for biased strand distribution p-value = 1.04e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767305‑2767571
|
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑ca‑ccc > 2:663818/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cccc < 1:604178/139‑1 (MQ=255)
gTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cccccc < 2:374367/139‑2 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGt < 1:1236535/139‑1 (MQ=255)
atgatgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca > 2:136104/1‑131 (MQ=255)
atgatgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca < 1:136104/131‑1 (MQ=255)
atgatgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca < 1:1585025/131‑1 (MQ=255)
atgatgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca > 2:1585025/1‑131 (MQ=255)
atgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cccccct < 2:1460218/124‑3 (MQ=255)
atgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cccccct > 1:1460218/1‑122 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cc > 1:687088/1‑115 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cc < 2:687088/115‑1 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑a > 1:1297033/1‑139 (MQ=255)
cAATTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑Aaca > 1:1491436/1‑139 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca < 2:1228195/118‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca > 1:1228195/1‑118 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTc > 1:1411621/1‑123 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTc < 2:1411621/123‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACg > 1:1435930/1‑139 (MQ=255)
tCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGtt > 2:1472178/1‑139 (MQ=255)
tCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGtt < 2:1435930/139‑1 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTccc < 1:1472178/139‑1 (MQ=255)
cAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTcccc < 2:1491436/139‑1 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCtgt > 1:894227/1‑139 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCtgt < 2:1028134/139‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCtgtg < 2:1297033/139‑1 (MQ=255)
ttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCAcc < 2:894227/139‑1 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCTCCCCA‑TCACAACGACCTGCATACTC‑ACCACGttttgatctgtgaactc > 2:213259/1‑126 (MQ=255)
tGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATATGG‑AACCCGTTTTCCCCTGTGCTCCCAc > 1:608156/1‑139 (MQ=255)
tctttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c > 2:37398/1‑80 (MQ=255)
tctttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c < 1:37398/80‑1 (MQ=255)
tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:608156/139‑1 (MQ=255)
ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCa < 2:1510509/86‑1 (MQ=255)
ccAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCa > 1:1510509/1‑86 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca > 2:342559/1‑65 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca < 1:342559/65‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑CC‑CCCCC‑TCACACAACCCTGCACAGGGAAACAC‑CTTTCCCATCTGCACCCACGACCCAATTTACCCCACATCAAACATCCCaattaaca > 2:916152/1‑134 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAAc > 1:1313387/1‑64 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAAc < 2:1313387/64‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTc < 1:144407/67‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTc > 2:144407/1‑67 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGtttt > 2:787087/1‑87 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGtttt < 1:787087/87‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTccc < 1:30428/90‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTccc > 2:30428/1‑90 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCa < 2:1486355/101‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCa < 1:49031/101‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCa > 1:1486355/1‑101 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCa > 2:49031/1‑101 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cc > 2:1333063/1‑53 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑cc < 1:1333063/53‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCACCTCC‑TCACAACTTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCCTGACTACATTTCCCCCCCTTTAAACTTCTCCATAATGt > 1:985425/1‑139 (MQ=255)
tttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGt < 1:57774/61‑1 (MQ=255)
tttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGt > 2:57774/1‑61 (MQ=255)
ggCATGATATTAACTTGTCCAATATGATCAAATAGCATG‑AACCC‑CCCCC‑ACACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTACCCCCCCTTTAAACTTCTCAATAATGTCACCAAtt < 1:916152/139‑1 (MQ=255)
tCCAATATGATCAAATAGCCTTAAA‑CC‑ACCCC‑TCACAACGTCCTGCATAGGG‑CACACGTTTTACCCTGTCCACCCACCACTAAATTCCCCCCCCTCTAAACTTCTCAAAAATGTCACCAATTTTCTGGAAATCCTacga > 1:646019/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATTAAA‑CC‑CCCCC‑TCATAACGTCCTGCATAGGT‑AACACGTTTTCCCCCGTGCACATACGACTAAATTTCCCCCCCTTTAAACCTTTCAATAATGCCACCAAATTTCTGGAAATCCTatga > 1:435206/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca < 1:942434/37‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑CCCCC‑Tcaca > 2:942434/1‑37 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑CC‑CCCCCATCACAACTTCCTTCATAGGG‑AACACGCTTTGCCCTGTGCACCCACCACTAAATTTCACACCCTTTAAAATTCTCAATAATGCCACCAATTTTCTGGaacacacatca > 2:1491890/1‑130 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑CC‑CCCCCATCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTTTGCACCCCAGACTAAATTTACCCCCCTTTAAACATCTCCATAATGTCACCAAATTTCTGGAATTACTagta > 2:1470604/1‑136 (MQ=255)
tGATCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTGCCCCCCCTTTAAACTTCTCAATAATGTCACCCATTTTCTGGAAATCCTATGATGCCttt < 1:1491890/139‑1 (MQ=255)
cagaaaTAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 2:289598/136‑1 (MQ=255)
aTCAAATAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 2:985425/139‑1 (MQ=255)
tAGCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa < 2:144910/139‑1 (MQ=255)
aggCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa < 2:1228727/137‑1 (MQ=255)
gCATT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAAt > 1:554388/1‑139 (MQ=255)
aTT‑AACCC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCCCTAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATgg > 2:1543356/1‑139 (MQ=255)
|
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑CCCCC‑TCACAACGTCCTGCATAGGG‑AACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767305‑2767571
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
