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 |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,688,036 |
T→C |
100% |
I43V (ATT→GTT) |
yfhG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,688,036 | 0 | T | C | 75.0%
| 57.3
/ 16.5
| 32 | I43V (ATT→GTT) | yfhG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (7/1); new base C (7/17); total (14/18) |
| Fisher's exact test for biased strand distribution p-value = 1.03e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGC > W3110S.gb/2687970‑2688094
|
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActt < 1:2568430/69‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActt < 1:2124564/69‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActt < 1:22488/69‑1 (MQ=255)
ttGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttc < 1:3086818/69‑1 (MQ=255)
aGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttctt < 1:3582536/67‑1 (MQ=255)
gcgcCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTctg < 1:1845351/69‑1 (MQ=255)
ccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTgg < 1:3240074/69‑1 (MQ=255)
gATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt < 1:2945365/54‑1 (MQ=255)
gATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt < 1:1902048/54‑1 (MQ=255)
gATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt < 1:2389692/54‑1 (MQ=255)
gATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt < 1:2131900/54‑1 (MQ=255)
gATGTCGCTACATTCAGTAGAAAGATAGTCACCCAGTTGATAAACCGGAActtt < 1:3643544/54‑1 (MQ=255)
gTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATc > 1:3145300/1‑69 (MQ=255)
gTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATc < 1:3693618/69‑1 (MQ=255)
gCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCaa < 1:1683981/68‑1 (MQ=255)
tCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTgg > 1:373681/1‑53 (MQ=255)
cAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATggctggct > 1:2008572/1‑69 (MQ=255)
cAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATggctggct > 1:3130557/1‑69 (MQ=255)
cAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAAtggctgg > 1:1217375/1‑67 (MQ=255)
gTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTa > 1:2755669/1‑69 (MQ=255)
gAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtg < 1:1038914/69‑1 (MQ=255)
gAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtg < 1:3688548/69‑1 (MQ=255)
aaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtgtg > 1:3334351/1‑69 (MQ=255)
aaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtgtg < 1:2187664/69‑1 (MQ=255)
aaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtgt < 1:3015010/68‑1 (MQ=255)
aGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtgt < 1:2280771/67‑1 (MQ=255)
aGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATtgt < 1:1576512/67‑1 (MQ=255)
tAGTCAGCCAGTTGATAAACCGGAACTTTttcttc < 1:751611/35‑1 (MQ=255)
ccAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTg < 1:2214290/64‑1 (MQ=255)
ccAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTg < 1:3653377/64‑1 (MQ=255)
cAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTa > 1:369350/1‑52 (MQ=255)
cAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTa > 1:581752/1‑52 (MQ=255)
tGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATggctggct > 1:3446040/1‑46 (MQ=255)
gATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAccc > 1:3526156/1‑68 (MQ=255)
gATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAccc > 1:2890383/1‑68 (MQ=255)
gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCa < 1:2225599/64‑1 (MQ=255)
gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCa < 1:525414/64‑1 (MQ=255)
tAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGc > 1:3149532/1‑69 (MQ=255)
tAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGc > 1:677068/1‑69 (MQ=255)
aaaCCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGc < 1:3680399/68‑1 (MQ=255)
|
TACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGC > W3110S.gb/2687970‑2688094
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
