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
|
71 |
51.6 |
2219666 |
95.9% |
2128659 |
118.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,806,042 |
(C)6→7 |
coding (42/759 nt) |
ydiY ← |
acid‑inducible putative outer membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,806,036 | 1 | . | C | 97.5%
| 142.5
/ ‑4.1
| 40 | G16G (GGC→GGG) | ydiY | acid‑inducible putative outer membrane protein |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base C (19/20); minor base T (0/1); total (19/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.38e-01 |
GGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGA > NC_000913/1805901‑1806165
|
ggagCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑‑ccc > 2:748215/1‑139 (MQ=255)
tttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGT‑CCCCCCGc < 1:897241/139‑1 (MQ=255)
tgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACa < 2:985872/126‑1 (MQ=255)
tgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACa > 1:985872/1‑126 (MQ=255)
cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGaa < 2:829663/139‑1 (MQ=255)
cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGaa > 1:938504/1‑139 (MQ=255)
cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGaa < 1:357246/139‑1 (MQ=255)
ttCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGc > 1:925011/1‑139 (MQ=255)
cAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCtt < 2:462291/139‑1 (MQ=255)
cTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATc > 2:277420/1‑139 (MQ=255)
ttCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa < 1:1027522/139‑1 (MQ=255)
cGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAag > 2:25977/1‑139 (MQ=255)
gTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGaa < 1:346573/106‑1 (MQ=255)
gTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGaa > 2:346573/1‑106 (MQ=255)
ttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTacaa < 2:925011/139‑1 (MQ=255)
gcTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACaaaa > 1:371493/1‑139 (MQ=255)
cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCa < 1:1050699/113‑1 (MQ=255)
cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCa > 2:1050699/1‑113 (MQ=255)
cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑‑cccccccg > 2:972570/1‑72 (MQ=255)
cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑‑cccccccg < 1:972570/74‑3 (MQ=255)
atcCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATc > 2:336644/1‑139 (MQ=255)
tcCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATcg < 2:811210/139‑1 (MQ=255)
ccATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATcgc > 2:891019/1‑139 (MQ=255)
aCAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTcc > 1:468789/1‑139 (MQ=255)
aGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCg > 2:198241/1‑139 (MQ=255)
aGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCg > 2:584455/1‑139 (MQ=255)
tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTccc > 1:455905/1‑136 (MQ=255)
tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTccc < 2:455905/136‑1 (MQ=255)
tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGa < 1:277420/139‑1 (MQ=255)
atcatcGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACg < 1:576487/53‑1 (MQ=255)
atcatcGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACg > 2:576487/1‑53 (MQ=255)
atcatcGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTa < 2:13/139‑1 (MQ=255)
catcGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAg < 1:198241/139‑1 (MQ=255)
tcGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa < 1:1016762/84‑1 (MQ=255)
tcGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa > 2:1016762/1‑84 (MQ=255)
cGGCAGCTGCATTCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGAt > 1:1094583/1‑139 (MQ=255)
ttCAGTGACGCAAACATGCCCCCCCCGCCAACATAACGATGGCTGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATTGCAGTCCCGGAAACTTTCTTAGGGATCACAGATTAg < 1:721343/139‑1 (MQ=255)
tCAGTGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCg < 2:468789/139‑1 (MQ=255)
tGACGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTccc > 2:112009/1‑139 (MQ=255)
cGCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTgg < 1:336644/139‑1 (MQ=255)
gCAAACATGC‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGa < 1:891019/139‑1 (MQ=255)
cAAACATGC‑CCCCCCGCCAACATAACGATGACAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGa > 1:108334/1‑117 (MQ=255)
cAAACATGC‑CCCCCCGCCAACATAACGATGACAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGa < 2:108334/117‑1 (MQ=255)
|
GGAGCTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGA > NC_000913/1805901‑1806165
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
