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 |
790,744 |
T→C |
100% |
N320N (AAT→AAC) |
dadA → |
D‑amino acid dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 790,744 | 0 | T | C | 76.4%
| 51.2
/ 10.5
| 42 | N320N (AAT→AAC) | dadA | D‑amino acid dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (2/8); new base C (32/0); total (34/8) |
| Fisher's exact test for biased strand distribution p-value = 3.81e-07 |
| 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. |
AAATCGCCATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAGATTGTTGGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTATCCA > minE/790677‑790804
|
aaaTCGCCATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAGATTGTTGGTTTTAAt < 1:1136045/68‑1 (MQ=255)
aaaTCGCCATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAGATTGTTGGTTTTAAt < 1:2908368/68‑1 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:801754/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:3098337/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:2918980/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:279888/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:2778845/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:2719050/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:2645235/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:3118505/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:3216193/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:2239231/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:2218896/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:3269896/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:3316963/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:1729656/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:167397/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:1655589/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:354175/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:1509719/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:738270/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:1257534/1‑69 (MQ=255)
ccATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGc > 1:1177733/1‑69 (MQ=255)
gTTTCGATAACCGCATTGGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:2327504/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:3223573/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:3322083/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:742356/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:817611/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:3058790/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:3037447/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:2449429/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:2238200/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:1284886/1‑69 (MQ=255)
gTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAAATTGTTGGCTTTAACACCGAGCTGTTGCAAc > 1:1249744/1‑69 (MQ=255)
gCGGAGATTGTTGGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTcgc > 1:2052026/1‑69 (MQ=255)
gCGGAGATTGTTGGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTcgc > 1:1639341/1‑69 (MQ=255)
tgttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTa < 1:2968851/69‑1 (MQ=255)
tgttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTa < 1:1741087/69‑1 (MQ=255)
tgttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTa < 1:1670272/69‑1 (MQ=255)
tgttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTa < 1:3435551/69‑1 (MQ=255)
tgttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTa < 1:1099859/69‑1 (MQ=255)
tgttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTGCGCGATCTCTa < 1:2490906/69‑1 (MQ=255)
gttgGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTa < 1:1033937/68‑1 (MQ=255)
ggTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTATCCa < 1:3174548/69‑1 (MQ=255)
|
AAATCGCCATTACCCGTTTCGATAACCGCATTCGTGTTGGCGGAATGGCGGAGATTGTTGGTTTTAATACCGAGCTGTTGCAACCGCGTCGTGAAACGCTGGAGATGGTGGTTCGCGATCTCTATCCA > minE/790677‑790804
|
| 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
