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 |
|
A3 F1 I1 R1
|
781 |
46.9 |
2231650 |
93.5% |
2086592 |
109.0 |
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 | 89.2%
| 110.1
/ 5.9
| 37 | 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 . (4/0); new base C (12/21); total (16/21) |
| Fisher's exact test for biased strand distribution p-value = 2.76e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767301‑2767571
|
aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑aag > 2:312355/1‑138 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑aaaac > 1:379811/1‑136 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c < 1:1057442/139‑1 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c < 1:992939/139‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑cc > 2:971657/1‑139 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑cc > 2:594982/1‑139 (MQ=255)
tGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑cccc > 1:599102/1‑139 (MQ=255)
ccGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTc < 1:594982/139‑1 (MQ=255)
gatgatGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCt < 1:971657/139‑1 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAac < 1:1072611/139‑1 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑ccccctca < 2:310878/115‑5 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑ccccctca > 1:310878/1‑111 (MQ=255)
cTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCACAGGGAACACGtttt > 1:204102/1‑139 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑CC‑C‑CCCC‑TCACAACATCCTGCATACGGAACACGTATTccc > 2:605122/1‑139 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑Tcaca < 1:250497/107‑1 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑Tcaca > 2:250497/1‑107 (MQ=255)
tGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgt < 2:599102/139‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg < 2:204102/139‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑c < 2:20497/97‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑c > 1:20497/1‑97 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑c > 1:795967/1‑92 (MQ=255)
tttGAAACTCTTCTTCCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑c < 2:795967/92‑1 (MQ=255)
aaaCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑c < 1:723326/88‑1 (MQ=255)
aaaCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑cc‑c‑c > 2:723326/1‑88 (MQ=255)
tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑ccc < 1:195202/139‑1 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTc > 1:504698/1‑88 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTc < 2:504698/88‑1 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑CACCCC‑TCACAACGTCCTGCATAGTGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑cccccc > 1:881695/1‑139 (MQ=255)
aaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑C‑CCCCATCAAAACGACTTACATACGGAAAACGTTTTCCCATGTGCACCCTCAATTAAATTT‑ccccccc > 2:195202/1‑139 (MQ=255)
aaCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTa < 1:312355/139‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:863062/105‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc > 2:863062/1‑105 (MQ=255)
cAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCCTTTaaa < 2:213571/139‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑CC‑C‑CACC‑TCAAACCGTCCTGCATAGGGAACAAGATTTACCCTGTGCACCAACGACTAAATTT‑CCACACCTATAAACTTCTCaaaaacat > 1:997307/1‑136 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑Tcaca > 2:1084734/1‑62 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑Tcaca < 1:1084734/62‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAac < 2:410317/80‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAac > 1:410317/1‑80 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg > 1:196647/1‑95 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg < 2:196647/95‑1 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 2:997307/139‑1 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CCGC‑CCCT‑TAACAACGGCATACATAGGCAACACGTTTTCTCAACTACAACCACGACTAAATTT‑ACCCCGCTTTAAACTTCCCAATAATCACACCaactaactca > 2:1005315/1‑131 (MQ=255)
ttAACTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGaaa < 1:605122/139‑1 (MQ=255)
aaCTTGTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATc < 2:881695/139‑1 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑Tcaca < 2:468944/38‑1 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑Tcaca > 1:468944/1‑38 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:863099/65‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTccc > 2:863099/1‑65 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACAAATTTTCTGGAAATCCTatga > 1:1063822/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑CCAA‑CCCC‑TAACAACGTTCTGCATAGGGAAAAAGTTTTACCCCGTGTACCCAAGACTACATTT‑CCCCCCCTTTAAAATTTTCAATAATATCACCCATTTTCTGCAAATCCTatga > 1:515907/1‑139 (MQ=255)
tatGATCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCt < 2:515907/139‑1 (MQ=255)
tCAAATAGCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCGTAGGGGACACGCTTTCCCCTGTGCACGCACGACTAAATTT‑CCCCCCCTTGAAGCTTCTCAATAATGACCGCAATTTTCTGGAAACCCCATAATGCCTTTccc > 2:530144/1‑139 (MQ=255)
gCATT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAAt < 2:1063822/139‑1 (MQ=255)
aTT‑AACCC‑C‑CCCC‑TCACAACGTCCTGCATATGGAACACGTTTTCCCCTGTGCACTCACGAATAAATTT‑CCCCCCCTTTGAACTTTTCACTAATGTCACCAATTTTCTGGAATTTCTATGATGCCTTTCCAGGTAAATgt > 2:28235/1‑138 (MQ=255)
aTT‑AA‑CC‑CACCCC‑TCACAACGTCCAGCATAGGGAAAACGCTTTCCCCCGTGCACCCACGACTAAATAT‑CCCCCCCTTTAAATTTCCCACTATTGTCACCAATTTACTGTACATCCTATGATGCCTGTCCCGGTAAGTgg > 1:182484/1‑139 (MQ=255)
|
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑CC‑C‑CCCC‑TCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑CCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGG > NC_000913/2767301‑2767571
|
| 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
