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 |
|
A10 F1 I1 R1
|
759 |
65.2 |
3386260 |
90.7% |
3071337 |
101.6 |
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 | 88.6%
| 126.9
/ 9.0
| 44 | 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 . (4/1); new base C (16/23); total (20/24) |
| Fisher's exact test for biased strand distribution p-value = 1.60e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAA > NC_000913/2767301‑2767567
|
aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c > 1:1121746/1‑139 (MQ=255)
ccTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c < 2:1680269/139‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑cc > 2:117592/1‑139 (MQ=255)
ctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑a‑c‑c‑cac > 1:1200677/1‑137 (MQ=255)
tctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAAGCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACaa > 1:1523338/1‑139 (MQ=255)
ctcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAAc < 1:446927/139‑1 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCTTGc < 2:1091115/133‑1 (MQ=255)
aCGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGc > 1:1091115/1‑133 (MQ=255)
cGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGa < 1:435267/139‑1 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑cc < 1:1326997/114‑1 (MQ=255)
gCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑cc > 2:1326997/1‑114 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAAGCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAac < 2:1523338/139‑1 (MQ=255)
ccAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAac < 2:23520/139‑1 (MQ=255)
cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTc > 1:1480645/1‑125 (MQ=255)
cAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTc < 2:1480645/125‑1 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca > 2:1477594/1‑118 (MQ=255)
aGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca < 1:1477594/118‑1 (MQ=255)
gTCAATGGATTTTTGAATCTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca < 2:1648697/112‑1 (MQ=255)
gTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca > 1:1648697/1‑112 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCtgtg > 1:889685/1‑139 (MQ=255)
ttttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 2:889685/139‑1 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAccc < 1:117592/139‑1 (MQ=255)
tcttcctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca > 2:16131/1‑90 (MQ=255)
tcttcctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca < 1:16131/90‑1 (MQ=255)
tctAAACGAAGCAGGATTCAATTCGGCCTTTTGGCATGATCTTAACTTGTCCAATATGATCCAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGAATAAATTTccc < 2:325200/139‑1 (MQ=255)
tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAGCGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAAATTccc < 2:1121746/139‑1 (MQ=255)
aaCCACTATATAATTCCCCCTTTTTCCATCATTTTAACTTTTCCCCTATTATTCAATCCCCTTCAC‑C‑C‑C‑CCC‑CCCCCCACCTCCTCCATAGGGAACACCTTTTCCCCTGTTCCCCCTCGACTAAATTTCCCCCCCTTTa < 2:1016309/139‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca < 1:1431100/77‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTcaca > 2:1431100/1‑77 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑ccc‑cc < 1:493586/60‑2 (MQ=255)
ttCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑ccc‑cc > 2:493586/1‑59 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑C‑C‑C‑CCC‑CTCACAACGTCTCGCATAGGGAACACGTTTACCCCTGTACACCCACGCCTAAATTTCCCCCCCTCTACACTTACCACTAATGt > 2:1593884/1‑139 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTCAACtt > 2:1200/1‑128 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACtt < 1:1200/128‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑ccc‑cctc > 2:614669/1‑56 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑c‑c‑c‑ccc‑cctc < 1:614669/59‑4 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑C‑CCCTCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGt > 1:23269/1‑139 (MQ=255)
atatTAACTTGTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 1:930363/139‑1 (MQ=255)
tatTCACTTGTCCAAAATGATGAAATAGCCTT‑AA‑C‑CTC‑CCC‑CACACATCATACTGCATGTGGAGCACGTTTTCCCCTGTGCTCCCCCGACTAAAGTTCCCCCCCTTTAAACTTGTCAATAATGTCACCAATTTTCTGGa < 2:1200677/139‑1 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:353233/66‑1 (MQ=255)
gTCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTccc > 2:353233/1‑66 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCTCAACGt < 2:384616/41‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCa < 2:761871/47‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCa > 1:761871/1‑47 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt < 1:1017832/81‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACt > 2:1017832/1‑81 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg < 1:1116934/128‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTgg > 2:1116934/1‑128 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga > 2:784512/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGACACCAATTTTCTGGAAATCCTatga > 2:209359/1‑139 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑CAC‑C‑CCC‑CTCACAGCGTCTAGCATAGGGAATACGTTTTAACCTATGCACCCACGACTAAATTACACCCCCTTTAAACTCCTCAATAATCTCACCAATTTTCTTAAAAACCTatgc > 1:722848/1‑138 (MQ=255)
tCCAATATGATCAAATAGCATT‑AA‑C‑C‑CTCCC‑CTCACAACGt > 1:384616/1‑41 (MQ=255)
tatGATCAAATAGCATT‑AA‑C‑C‑C‑CCCTCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCt < 2:23269/139‑1 (MQ=255)
tCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAac > 2:468003/1‑45 (MQ=255)
tCAAATAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAac < 1:468003/45‑1 (MQ=255)
tAGCATT‑AACC‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa < 1:784512/139‑1 (MQ=255)
|
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑C‑C‑C‑CCC‑CTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAA > NC_000913/2767301‑2767567
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ 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
