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 I1 R1
|
759 |
71.0 |
3673240 |
91.5% |
3361014 |
104.6 |
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 | 89.7%
| 117.6
/ 6.0
| 40 | 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 . (3/1); new base C (11/24); total (14/26) |
| Fisher's exact test for biased strand distribution p-value = 1.23e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
| * | NC_000913 | 2,767,438 | 2 | . | C | 85.0%
| 112.3
/ 13.0
| 40 | 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 . (3/3); new base C (11/23); total (14/26) |
| Fisher's exact test for biased strand distribution p-value = 6.46e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑CCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTC > NC_000913/2767300‑2767560
||
aaGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑a‑‑a > 1:1674047/1‑139 (MQ=255)
ctctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc > 2:767222/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑c > 1:713450/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc < 2:1432929/138‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc > 1:1432929/1‑138 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTAGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑c > 1:555445/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc > 2:1178662/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTAAAGAATTCGCCCTTTTGGCATGATATTAAATTGTCCAATATAATCAAATAGAATT‑A‑‑A‑‑cccc‑‑cc > 1:234024/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGCCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc > 1:1529210/1‑139 (MQ=255)
ctGTTTTGTCCCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc > 2:1789826/1‑139 (MQ=255)
gTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑cc > 1:314398/1‑138 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑AC‑CCCC‑‑CC‑‑CTc‑‑aca < 1:985783/139‑1 (MQ=255)
tctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑ccctcaca < 2:314398/139‑8 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGt < 2:1674047/139‑1 (MQ=255)
cGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTc < 1:1380984/139‑1 (MQ=255)
atgTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATATAATTCGCCCTTTTGGCATGAAATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCa < 1:905631/139‑1 (MQ=255)
gTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATa < 1:1789826/139‑1 (MQ=255)
cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAac > 2:1427793/1‑139 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑cc > 2:1745901/1‑112 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑cc < 1:1745901/113‑2 (MQ=255)
tGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGtttt < 2:498667/139‑1 (MQ=255)
gTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CCC‑‑ACAACATCATGCATCAGGAACACGTCTTc > 2:538889/1‑139 (MQ=255)
gTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑CCCCCACC‑‑CTC‑‑ACAACGTCGAGAATTGTGAGCACGttttg > 1:1359342/1‑138 (MQ=255)
cAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTccc < 1:1427793/139‑1 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc > 2:844672/1‑98 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc < 1:844672/98‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑ccctcaca < 2:473593/107‑8 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑ccctcaca > 1:473593/1‑100 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCATTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:234024/139‑1 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑TCAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:555445/139‑1 (MQ=255)
tGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑ccctcaca < 2:606167/100‑8 (MQ=255)
tGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑cccc‑‑cc‑‑ccctcaca > 1:606167/1‑93 (MQ=255)
ctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 2:1312313/139‑1 (MQ=255)
tAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTcccc < 1:587201/139‑1 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑CCAC‑‑CC‑‑CTCTAACACCTACCTGCATCGGGAAACCTTTTTCCCCTTTGTACCCCTGACTAAATTTccccc > 2:1399118/1‑139 (MQ=255)
cAGTATAGAATTCGGCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACATCGACCTGCATAGGGAACACGTTTTCCCCTTTGCACCCACGACTAGATTTCCCCCCCTTTcaa < 1:620848/139‑1 (MQ=255)
cAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTaaa < 2:1359342/139‑1 (MQ=255)
aGTATAGAATTAGCCCATTTGGCATGATATTAACGTGTCCAATATGATCAAATAGCATT‑A‑‑ATCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAAc < 1:1399118/139‑1 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGtttt < 2:710061/91‑1 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGtttt > 1:710061/1‑91 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTACATATGAAACACGTTTTCCCCTGTGCACCCACGACAACATTTCCCACACCATACACTTCTCaata > 2:228272/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATa > 2:685511/1‑75 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATa < 1:685511/75‑1 (MQ=255)
tttGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑CCCC‑‑CCCTCTC‑‑ACAATGTCCTCAATAGTGAAGGCGTTTTCCCCTGTGCACCAACGACTAATTTTCCCCCCTTTGAAACTGCTCAATAATGTCAcc > 1:76629/1‑139 (MQ=255)
gATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCt < 2:713450/139‑1 (MQ=255)
atatTAACTTGTACAATATGATCAAAGAGCTTT‑ATCC‑‑CCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGTAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAATCTTCTCAATAATGTCACCAATTTTCTg < 1:1178662/139‑1 (MQ=255)
atTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGa < 2:318648/139‑1 (MQ=255)
tCCAATATGATCAAATAGCATTAA‑‑A‑‑CCCC‑‑AC‑‑CTC‑‑ACAACGCCCTTCATAGCGAACACGTTTTCCACAGTCCACCCACGACTAAATTTCTCCCACTTGCAACTTATCAATAAAGTCACCAATTTTCTTGAATTCATatga > 2:747038/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGa > 1:95601/1‑54 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGa < 2:95601/54‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTccc < 2:1032042/66‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTccc > 1:797643/1‑66 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTccc < 2:797643/66‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTccc > 1:1032042/1‑66 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTc > 1:783790/1‑64 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTc < 2:783790/64‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACCTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatg > 1:824613/1‑139 (MQ=255)
cagaaTATGATCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGCAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatg < 2:1213280/136‑1 (MQ=255)
gATCAAATAGCATT‑A‑‑AC‑CCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc < 1:747038/139‑1 (MQ=255)
tCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGtttt > 1:1350586/1‑53 (MQ=255)
tCAAATAGCATT‑A‑‑ACCCCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCAGAGGGAACACGtttt < 2:1350586/53‑1 (MQ=255)
||
AAGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑A‑‑A‑‑CCCC‑‑CC‑‑CTC‑‑ACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTC > NC_000913/2767300‑2767560
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
