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 |
|
A13 F1 I1 R1
|
778 |
68.7 |
3228504 |
93.4% |
3015422 |
109.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,767,445 |
(C)7→9 |
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 | 83.3%
| 116.0
/ 16.4
| 42 | 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 . (5/2); new base C (14/21); total (19/23) |
| Fisher's exact test for biased strand distribution p-value = 2.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
| * | NC_000913 | 2,767,438 | 2 | . | C | 82.9%
| 115.0
/ 16.5
| 41 | 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 . (5/2); new base C (13/21); total (18/23) |
| Fisher's exact test for biased strand distribution p-value = 2.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCG > NC_000913/2767305‑2767563
||
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑Aa‑‑cc‑a‑c‑‑c > 2:538825/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc > 1:1182665/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ac‑c‑c‑‑cc > 2:1457008/1‑139 (MQ=255)
ttttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc‑‑ccc < 2:1182665/139‑3 (MQ=255)
ttttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc‑‑ccc > 2:1303059/1‑137 (MQ=255)
ttttGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc‑‑ccc < 2:1417033/139‑3 (MQ=255)
tGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CC‑C‑C‑‑CC‑‑C‑‑T‑‑caca < 2:1220730/139‑1 (MQ=255)
tctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc‑‑ccctcaca < 1:1278360/139‑8 (MQ=255)
cccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCACGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACg > 2:166299/1‑139 (MQ=255)
cGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTc > 1:1391263/1‑139 (MQ=255)
gTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATa < 2:1329542/139‑1 (MQ=255)
gTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑c < 2:589466/118‑1 (MQ=255)
gTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑c > 1:589466/1‑118 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGt > 2:307983/1‑129 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGt < 1:307983/129‑1 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c < 2:232935/114‑1 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c > 1:232935/1‑114 (MQ=255)
cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAac < 1:1303059/139‑1 (MQ=255)
cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAac < 1:620359/139‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc‑‑ccctcaca < 2:957870/118‑8 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc‑‑ccctcaca > 1:957870/1‑111 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc < 1:898449/110‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc > 2:898449/1‑110 (MQ=255)
gTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CCAC‑C‑‑CCA‑C‑‑T‑‑CAAATCGTCTTGCATAGGGTACACGTTTTc > 1:1431920/1‑139 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGt < 1:679133/111‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGt > 2:679133/1‑111 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTccc > 2:189758/1‑135 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTccc < 1:189758/135‑1 (MQ=255)
ctctTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCACGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt < 1:166299/139‑1 (MQ=255)
ctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:1188348/139‑1 (MQ=255)
aggTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa < 2:688549/137‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑‑CC‑CAC‑‑CC‑‑C‑‑T‑‑CACAACGTCACGCATAGGGAACACGATTTACCTTGTGCACCCACCACTAAATTTCCCCCCCTCAAAACGTCCCATTTATg > 1:515637/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CCCAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTtcc > 1:861358/1‑116 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTc < 2:861049/68‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTc > 1:1194319/1‑68 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTc < 2:1194319/68‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTc > 1:861049/1‑68 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGttt < 1:1561684/87‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGttt > 2:1561684/1‑87 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 1:312641/1‑100 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:312641/100‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:861358/116‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑TC‑C‑C‑‑CCAGT‑‑T‑‑CCCAACTCCCTGCCTAGGCAACAAGTGTTTCCCTGTGCTCCCAAGACAAAATTTCCCCCCCTTTCACCTTCTCAATAATg > 2:184506/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CC‑C‑C‑‑CC‑‑C‑‑TTCCATAACGTACTCCTTAGTGAAAACGGTTTCCACTGTCCACCCACGCCTAAATTCCCCCCCCTTTCAACTCCTCcataata > 1:859514/1‑138 (MQ=255)
ccTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc > 1:236859/1‑53 (MQ=255)
ccTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑cc‑c‑c‑‑cc < 2:236859/53‑1 (MQ=255)
tGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTc < 2:859514/139‑1 (MQ=255)
atTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CC‑C‑C‑‑CC‑‑CCTT‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGa < 1:184506/139‑1 (MQ=255)
tAACTTGTCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGaaa < 2:1191681/139‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:1456403/75‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 2:1456403/1‑75 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGACGTGCATAGGGAACACGTTTTCCCCTCTGCACCCACGACTAGATTTCCCCCCC‑TTAAACTTCTCAATAATGTCACCAATTTTCTCGAAATACTatga > 2:836839/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑C‑‑CCCAACGTCCTGCATAGAGAAAACGTTTTCCACCGTCCACCCACGACTAAACATCCCACCCTTCTCCCTCCCCACTAATCTCACCAATTTCCTGGCAATCCTatt > 1:621266/1‑138 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑A‑‑CACAACGTCCTCCATAGGGAAAAACTTTTACCCCGAGCACCCAAGACTAAAATTCACCCCCCTTAAACCTTTCAAAAATGACAACAATTTTTAGGCAAACCTata > 1:1281577/1‑138 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑‑CC‑C‑CCACC‑‑C‑‑T‑‑AACAACATCCAGCATAAGGAACACGATATTCTCTGGGCAACCACGACCAAATTTGACCCCCTTCGAAATTCGCAATAATATAACCAACTTTCGGGAAATACTata > 1:997578/1‑138 (MQ=255)
actattatCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACCACCTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTCAACTTCTCACTAATGTCACCAATTTTCTGGAAATCCTatgatg < 1:538825/137‑1 (MQ=255)
tatGATCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CAAAACGTCCTGCTTAGGGCACACGTTTTCCCCTGTGCACCCACGACTCAATTTCCCCCCCCTTAAACTTCTCAATAATGTCCCCCATTTTCTGGAAATCCAATGATGcc > 1:109959/1‑139 (MQ=255)
aTCAAATAGCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc < 2:621266/139‑1 (MQ=255)
cAAATAGCAGT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg < 1:836839/139‑1 (MQ=255)
aaaTATCATT‑AACCCC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg < 1:1457008/139‑1 (MQ=255)
||
TCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CC‑C‑C‑‑CC‑‑C‑‑T‑‑CACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCG > NC_000913/2767305‑2767563
|
| 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
