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 F17 I0 R1
|
71 |
95.7 |
2922988 |
91.7% |
2680379 |
65.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
814,839 |
G→A |
100% |
P85S (CCG→TCG) |
ispE ← |
4‑diphosphocytidyl‑2‑C‑methylerythritol kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 814,839 | 0 | G | A | 75.0%
| 103.9
/ 33.6
| 56 | P85S (CCG→TCG) | ispE | 4‑diphosphocytidyl‑2‑C‑methylerythritol kinase |
| Reads supporting (aligned to +/- strand): ref base G (9/5); new base A (42/0); total (51/5) |
| Fisher's exact test for biased strand distribution p-value = 5.24e-04 |
| 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. |
ATCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATCAACAATCGCGCTG > minE/814793‑814883
|
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGCCGCCCGCTGTCTGCCGCAGt > 1:419928/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAg > 1:395911/1‑70 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:253651/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2712440/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:257915/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1041950/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2728372/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2758624/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:278277/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2819731/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2829715/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2856966/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2860820/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2886912/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:303706/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:411246/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:429947/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:461410/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:607496/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:646368/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:676775/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:725587/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:750869/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:819051/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:971532/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2420440/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1110447/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1176872/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1362804/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1377697/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1422265/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1493610/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:151403/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1549378/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1799871/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:1863015/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2504585/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2380205/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2301918/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2278669/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2204026/1‑71 (MQ=255)
aTCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGAAAGACGCCCGCTGTCTGCCGCAGt > 1:2105632/1‑71 (MQ=255)
gCTGATATTCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATCAACAATCGCGCt > 1:1857950/1‑70 (MQ=255)
gCTGATATTCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATCAACAATCGCGCTg > 1:467813/1‑71 (MQ=255)
ttCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaac < 1:276582/54‑1 (MQ=255)
ttCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaac < 1:623730/54‑1 (MQ=255)
ttCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaac < 1:132832/54‑1 (MQ=255)
ttCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaac < 1:2104356/54‑1 (MQ=255)
ttCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaac < 1:2087581/54‑1 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:1556547/1‑54 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:1609174/1‑54 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:2290021/1‑54 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:1706591/1‑54 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:765121/1‑54 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:774012/1‑54 (MQ=255)
cGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATcaacaa > 1:782727/1‑54 (MQ=255)
|
ATCGGCAAACGCTTGTCAATGCTGATATTCGCACCGCTTCCCGTCGGAAGACGCCCGCTGTCTGCCGCAGTTTTCATCAACAATCGCGCTG > minE/814793‑814883
|
| 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
