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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
559,842 |
T→C |
67.6% |
V363V (GTT→GTC) |
cmr → |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 559,842 | 0 | T | C | 67.6%
| 74.2
/ 42.5
| 86 | V363V (GTT→GTC) | cmr | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base T (7/21); new base C (15/43); total (22/64) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCA > minE/559778‑559903
|
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGt > 1:2264656/1‑68 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGt > 1:144186/1‑68 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:989676/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:1833235/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:192464/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2039138/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2108126/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2226101/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2735010/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:1384995/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:3282427/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:500124/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:849286/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTATGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:1645494/1‑69 (MQ=255)
gCGATATGAGTAAAGGAACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:3096016/1‑69 (MQ=255)
aaGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCa < 1:2928285/69‑1 (MQ=255)
aaGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCa < 1:3408259/69‑1 (MQ=255)
aaGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATCCTGATCTTTACCGTTGGTATTGAAATCAGCa < 1:902227/69‑1 (MQ=255)
ggTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCaaa < 1:1344951/69‑1 (MQ=255)
ggTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCaaa < 1:2530259/69‑1 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:2959808/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:2877121/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:2201579/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:764325/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:1097881/1‑58 (MQ=255)
tACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATc > 1:1526301/1‑61 (MQ=255)
tACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACa > 1:3367192/1‑69 (MQ=255)
aCGGTTTCTGCCGCGATGGGAAGGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACAt < 1:2762531/69‑1 (MQ=255)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:144238/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2999204/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:3311067/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:424454/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:43417/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2289678/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:1765040/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:1444577/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2844028/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:717454/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:724569/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2077308/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:205025/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:907064/69‑1 (MQ=39)
tCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2146368/68‑1 (MQ=39)
tCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:3253842/68‑1 (MQ=39)
tCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGGTGGTATTGAAATCAGCAAACAt < 1:1639229/63‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:932955/62‑1 (MQ=39)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:2987115/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:487996/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:1287545/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:1826653/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:1273804/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:558748/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:595036/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:842780/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:988071/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:2153979/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:2711175/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:1815064/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:1744148/69‑1 (MQ=255)
gcgATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAAc < 1:2543056/69‑1 (MQ=255)
ggAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAAGGGGGGc < 1:438968/69‑1 (MQ=255)
ggAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGc < 1:1844479/69‑1 (MQ=255)
ggAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGc < 1:1125500/69‑1 (MQ=255)
gCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACgg < 1:1062531/60‑1 (MQ=255)
gCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACgg < 1:2141218/60‑1 (MQ=255)
gCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACgg < 1:825978/60‑1 (MQ=255)
gCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACgg < 1:1164585/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:1233409/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:831360/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:2124151/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:848225/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:1769943/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:706141/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:1696375/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:2550546/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:2590578/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:2607036/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:3149127/60‑1 (MQ=255)
gATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACt < 1:1669377/60‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:2782821/66‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:1275337/66‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:1770333/66‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:2607157/66‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:264999/66‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:1940272/66‑1 (MQ=255)
ccGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCa < 1:2670176/66‑1 (MQ=255)
|
GCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTGGCTGAACGGGGGCAACGGACTGTTTAATCTCTTCA > minE/559778‑559903
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
