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 |
|
A14 F1 I1 R1
|
770 |
68.5 |
3470224 |
91.7% |
3182195 |
103.4 |
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 | 88.9%
| 106.9
/ 5.9
| 36 | 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 (13/19); total (17/19) |
| Fisher's exact test for biased strand distribution p-value = 4.04e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGT > NC_000913/2767301‑2767565
|
aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c > 2:677567/1‑139 (MQ=255)
aGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c < 1:677567/139‑1 (MQ=255)
ctctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c < 2:584638/139‑1 (MQ=255)
ctctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c < 1:72601/139‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c‑c < 1:1515758/139‑1 (MQ=255)
tctGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c‑c < 1:73658/139‑1 (MQ=255)
gTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c‑cccc < 1:1118808/139‑2 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTcaca < 2:38498/139‑1 (MQ=255)
gTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTcaca < 1:444973/139‑1 (MQ=255)
ttccccGATGGTGTACGCCAAGTCCTGTCAAAGGATTTTTGAAACCCTTCTTTCTAAACGAACCAGTAAAGAATTCGCCCTTTTGGCATGATATTAACCTGTCCAATATGATCCAATAGCCTT‑AA‑‑ccc‑c‑ccccctcaca < 1:486274/136‑8 (MQ=255)
tcCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACg > 1:985656/1‑139 (MQ=255)
gTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAAA‑‑CCC‑C‑CCCTCACAACGTCCTGCATAAGGAacacat > 2:210695/1‑137 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTcc > 2:1410395/1‑139 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:985656/139‑1 (MQ=255)
tCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:811888/139‑1 (MQ=255)
cAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AACCCCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 1:1410395/139‑1 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTcaca > 1:578264/1‑106 (MQ=255)
ggATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTcaca < 2:578264/106‑1 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c‑cccc > 1:600662/1‑95 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c‑cccc < 2:600662/96‑2 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c > 2:909279/1‑92 (MQ=255)
tttGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑ccc‑c < 1:909279/92‑1 (MQ=255)
ctttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAac < 2:1148984/107‑1 (MQ=255)
ctttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c < 1:309820/77‑1 (MQ=255)
ctttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑c > 2:309820/1‑77 (MQ=255)
ctttctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CCCAC‑CCCTCACAACGTCCTGCATAGGGAac > 1:1148984/1‑107 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTcccccc > 2:1018128/1‑139 (MQ=255)
aaaCGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CCC‑CACCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTcccccc > 2:587810/1‑139 (MQ=255)
aaCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTa < 1:1426516/139‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCCCAACGTCCTGCATAGGGAac > 1:1457894/1‑95 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAac < 2:1457894/95‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTccc < 2:837285/105‑1 (MQ=255)
aCCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTccc > 1:837285/1‑105 (MQ=255)
gTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGATTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACtt < 1:453257/139‑1 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTc > 1:148505/1‑72 (MQ=255)
aaTTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTc < 2:148505/72‑1 (MQ=255)
cGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc > 2:699974/1‑116 (MQ=255)
cGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTccc < 1:699974/116‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACg < 2:786757/83‑1 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACg > 1:786757/1‑83 (MQ=255)
gCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAAAACAATATCCCCTGTGCACTCACGACTAAATTTCCCCCCCCTTAAACTTCTCattaaaat > 2:453257/1‑136 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACTTCCTGCATAGGGAACACGTTCTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACt > 1:1347993/1‑102 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGtttt < 1:1457644/62‑1 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGtttt > 2:1457644/1‑62 (MQ=255)
tCCAATATGATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACt < 2:1347993/102‑1 (MQ=255)
gATCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTc < 1:559018/139‑1 (MQ=255)
aTCAAATAGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGCGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTcc < 2:1344534/139‑1 (MQ=255)
aaTAGCATT‑AA‑‑CCC‑CACCCTCACAACGTCCTGCATAGGGAACACGTTTTACCCTGTGCACCCACGACTAAAATTCCCCCCCTTACAACTTCTCAATAATGTCACCTATTTTCTGGAAATCCTATGATGCCTTTCCCGGt > 1:1344534/1‑139 (MQ=255)
aGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc < 1:1532526/58‑1 (MQ=255)
aGCATT‑AAC‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCAcc > 2:1532526/1‑58 (MQ=255)
|
AGCCTCTGTTTTGTCTCCCGATGATGTACGCCAAGTCCTGTCAATGGATTTTTGAAACTCTTCTTTCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATT‑AA‑‑CCC‑C‑CCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCCCCTTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGT > NC_000913/2767301‑2767565
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
