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 I2 R1
|
67 |
27.9 |
1239648 |
95.3% |
1181384 |
112.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,871,308 |
G→A |
T158I (ACA→ATA) |
ispF ← |
2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,871,308 | 0 | G | A | 83.3%
| 49.1
/ 5.6
| 24 | T158I (ACA→ATA) | ispF | 2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase |
| Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (11/9); total (13/11) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
GAATATGCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTGTTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTC > NC_000913/2871172‑2871429
|
gAATATGCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTttatt > 2:457658/1‑139 (MQ=255)
tatGCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGcc < 1:457658/139‑1 (MQ=255)
gCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTa > 1:552300/1‑139 (MQ=255)
cccAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTGTTGCCTTAATGAGTAGCGCCACCGCTTCACAGGc < 1:605346/139‑1 (MQ=255)
cAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATg > 2:331395/1‑114 (MQ=255)
cAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATg < 1:331395/114‑1 (MQ=255)
ccGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATccc < 2:156811/139‑1 (MQ=255)
gCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTc > 2:479057/1‑139 (MQ=255)
cccGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTgg > 1:436604/1‑139 (MQ=255)
tGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCgtagta > 1:540257/1‑125 (MQ=255)
tGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCgtagta < 2:540257/125‑1 (MQ=255)
tttACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAAcat < 2:552300/139‑1 (MQ=255)
aGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAAcatc < 2:53432/130‑1 (MQ=255)
aGGTAAGTGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAAcatc > 1:53432/1‑130 (MQ=255)
tGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGt > 2:201146/1‑81 (MQ=255)
tGAGATTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGt < 1:201146/81‑1 (MQ=255)
gaTTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACg < 2:76529/112‑1 (MQ=255)
gaTTATCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACg > 1:76529/1‑112 (MQ=255)
aTCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACGGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCtt > 2:201987/1‑139 (MQ=255)
aTCAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCtt > 2:510626/1‑139 (MQ=255)
tCAAACTCAATCATTTTGTTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTc > 1:468349/1‑139 (MQ=255)
cAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATccc > 2:438428/1‑57 (MQ=255)
cAAACTCAATCATTTTATTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATccc < 1:438428/57‑1 (MQ=255)
tCATTTTGTTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTcc > 2:256839/1‑79 (MQ=255)
tCATTTTGTTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTcc < 1:256839/79‑1 (MQ=255)
|
GAATATGCTCACCTTCACCATCAGGCTCAAAGCCCAAATCTTCCACCACCACAAAGTCTTCCGGATTGGCTTTCAGCAGCCCGGTGCCTTGCGGTTTACCGTGGAGGTAAGTGAGATTATCAAACTCAATCATTTTGTTGCCTTAATGAGTAGCGCCACCGCTTCACAGGCAATCCCTTCCCCACGTCCGGTAAATCCCAGTTTTTCCGTAGTAGTGGCTTTCACGTTAACATCATCCATATGGCAGCCGAGATCTTC > NC_000913/2871172‑2871429
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
