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 |
|
A6 F1 I0 R2
|
251 |
90.0 |
5200563 |
86.9% |
4519289 |
59.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,768,269 |
A→G |
22.4% |
T143T (ACT→ACC) |
rluD ← |
23S rRNA pseudouridine synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,768,269 | 0 | A | G | 22.4%
| 108.8
/ 29.3
| 58 | T143T (ACT→ACC) | rluD | 23S rRNA pseudouridine synthase |
| Reads supporting (aligned to +/- strand): ref base A (19/26); new base G (9/4); total (28/30) |
| Fisher's exact test for biased strand distribution p-value = 1.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.80e-01 |
TCACGCCGTTGCAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTGGATAGTAA > minE/1768201‑1768335
|
tCACGCCGTTGCAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAgt > 1:1287926/1‑71 (MQ=255)
cGTTGCAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTc < 1:4881670/71‑1 (MQ=255)
gCAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCtt > 1:3805316/1‑69 (MQ=255)
gCAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCtt > 1:609592/1‑69 (MQ=255)
cAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTAt < 1:62579/71‑1 (MQ=255)
aaaGATTCGACTAAACGCGGCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATc < 1:856390/71‑1 (MQ=255)
aaGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATc > 1:4756628/1‑70 (MQ=255)
aaGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATc > 1:4937276/1‑70 (MQ=255)
aGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAg < 1:695043/56‑1 (MQ=255)
ttCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAgac < 1:2475481/71‑1 (MQ=255)
cGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGCTGTCTTTATCCAgacg < 1:1077922/70‑1 (MQ=255)
cTAACCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAgacgatg > 1:394098/1‑70 (MQ=255)
cTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAgacgatg > 1:333370/1‑70 (MQ=255)
aaaCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAgacgatggac > 1:1031982/1‑71 (MQ=255)
aaaCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAgacg < 1:4671128/65‑1 (MQ=255)
aaCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTCTTTATCCAgacgatggacg < 1:5192736/71‑1 (MQ=255)
aaCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTCTTTATCCAgacgatggacg < 1:668881/71‑1 (MQ=255)
aaCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTCTTTATCCAgacgatggacg < 1:3954815/71‑1 (MQ=255)
aaCGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTCTTTATCCAgacgatggacg < 1:674918/71‑1 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:3711781/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:3285407/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:4954626/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:895989/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:1172230/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:1234699/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:1385071/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCa > 1:223549/1‑52 (MQ=255)
tGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAgac < 1:2293377/55‑1 (MQ=255)
aGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCg < 1:1183548/68‑1 (MQ=255)
aGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCg < 1:3557312/68‑1 (MQ=255)
aGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCg < 1:1714990/68‑1 (MQ=255)
aGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCg < 1:4388085/68‑1 (MQ=255)
aGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCg < 1:2214542/68‑1 (MQ=255)
gCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCg < 1:4525035/67‑1 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:212814/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:953618/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:1875520/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:4935562/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:4920191/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:4475045/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:4067852/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:2440229/1‑40 (MQ=255)
ccGGAACGGTTTTTGCCACAACCATCAGGCCGGTGGTGTc > 1:2336165/1‑40 (MQ=255)
cGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCAcgc < 1:2866581/70‑1 (MQ=255)
ttGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGc < 1:1995938/70‑1 (MQ=255)
gCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAAt > 1:2989975/1‑71 (MQ=255)
gCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAAt > 1:3196140/1‑71 (MQ=255)
aaCCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTg < 1:1260436/71‑1 (MQ=255)
aaCCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTg < 1:697998/71‑1 (MQ=255)
aCCATCAGGCCATTTGTGTCTTTATCCAgacgatggac < 1:376026/38‑1 (MQ=37)
aCCATCAGGCCAGTTGTGTCTTTATCCAgacgatggac < 1:1920200/38‑1 (MQ=255)
aCCATCAGGCCAGTGGTGTCTTTATCCAgacgatggac < 1:1684132/38‑1 (MQ=255)
aCCATCAGGCCAGTGGTGTCTTTATCCAgacgatggac < 1:784046/38‑1 (MQ=255)
aCCATCAGGCCAGTGGTGTCTTTATCCAgacgatggac < 1:452299/38‑1 (MQ=255)
aCCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTg < 1:2327571/70‑1 (MQ=255)
tCAGGCCAGTGGTGTCTTTATCCAgacgatggacgat < 1:4966811/37‑1 (MQ=255)
aGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTGGATAGt < 1:3214185/70‑1 (MQ=255)
gCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTGGATAGTaa > 1:1635730/1‑70 (MQ=255)
|
TCACGCCGTTGCAAAGATTCGACTAAACGCGTCTGAGCCGGAACGGTTTTTGCCACAACCATCAGGCCAGTGGTGTCTTTATCCAGACGATGGACGATGCCCGCACGCGGTACATCGGCAATGGGTGGATAGTAA > minE/1768201‑1768335
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
